Supplementary Online Content
Ganz P, Heidecker B, Hveem K, et al. Development and validation of a protein-based risk score for cardiovascular outcomes among patients with stable coronary heart disease. JAMA. doi: 10.1001/jama.2016.5951
eTable 1. List of 1130 Proteins Measured by Somalogic’s Modified Aptamer-Based Proteomic Assay eTable 2. Coefficients for Weibull Recalibration Model Applied to 9-Protein Model eFigure 1. Median Protein Levels in Derivation and Validation Cohort eTable 3. Coefficients for the Recalibration Model Applied to Refit Framingham eFigure 2. Calibration Plots for the Refit Framingham Model eTable 4. List of 200 Proteins Associated With the Risk of MI, Stroke, Heart Failure, and Death eFigure 3. Hazard Ratios of Lasso Selected Proteins for Primary End Point of MI, Stroke, Heart Failure, and Death eFigure 4. 9-Protein Prognostic Model Hazard Ratios Adjusted for Framingham Variables eFigure 5. 9-Protein Risk Scores by Event Type
This supplementary material has been provided by the authors to give readers additional information about their work.
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Supplemental Material
Table of Contents 1 Study Design and Data Processing ...... 3 2 Table of 1130 Proteins Measured ...... 4 3 Variable Selection and Statistical Modeling ...... 62 4 Recalibration for Validation...... 63 5 Table of Individual Proteins Associated with Cardiovascular Risk ...... 67 5.1 Biological Functions of 16 LASSO-selected Proteins ...... 74 5.2 9-Protein Model Specification ...... 77 6 Risk Score Distributions by Event Type ...... 79 7 References ...... 80
List of Figures and Tables
eTable 1: List of 1130 proteins measured by SomaLogic’s modified aptamer-based proteomic assay. ______4
eTable 2: Coefficients for Weibull recalibration model applied to 9-protein model. ______64
eFigure 1: Median protein levels in Derivation and Validation cohort. ______65
eTable 3: Coefficients for the recalibration model applied to refit Framingham. ______66
eFigure 2: Calibration plots for the refit Framingham model. ______666
eTable 4: List of 200 proteins associated with the risk of MI, stroke, heart failure and death. ______67
eFigure 3: Hazard ratios of LASSO selected proteins for primary end-point of MI, stroke, heart failure and death. 76
eFigure 4: 9-protein prognostic model hazard ratios adjusted for Framingham variables. ______78
eFigure 5: 9-protein risk scores by event type. ______79
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1 Study Design and Data Processing The flowchart shown in Figure 1 in the main article describes the key steps in the development and validation of the 9-protein model discussed in the main manuscript. Protein measurements in plasma samples were generated over a period of 3 weeks in 32 separate assay runs. Study samples were randomly assigned to assay runs along with a set of calibration and control samples. No identifying information was available to the laboratory technicians operating the assay.
Intra-run normalization and inter-run calibration were performed according to assay data quality control (QC) procedures defined in the good laboratory practice (GLP) quality system of SomaLogic, Inc. Inter- run calibration removes “batch effects” between the successive assay runs by matching the median signal over replicate observations of a pooled plasma calibrator sample included in each assay run to a fixed signal level reference. Typical calibration scale factors are close to unity and quality control (QC) acceptance criteria specify the acceptable range of scale factors as the median scale factor ± 40%. Intra- run normalization controls for “bulk” signal intensity biases that can result from either differential hybridization efficiency or differential sample dilution (or other collection protocol artifacts) that change the total protein concentration in the sample. The former effect is captured by a set of controls used to monitor the hybridization reaction for each sample and the latter uses the median of the ratio of median signal levels in each sample to the median signal level for the modified aptamers over all samples within the run. Typical normalization scale factors are close to unity and quality control (QC) acceptance criteria requires normalization scale factors for a sample to fall in the range [0.4, 2.5]. Seventy-six of the original 1130 proteins measured failed the inter-run calibration QC metrics in at least one of the 32 independent assay runs and were considered technical (analytical) failures unfit for analysis. Samples failing the intra- run normalization quality control (QC) metrics were technical failures unfit for analysis. Hemolyzed samples have a distinctive pattern of extreme hemoglobin and haptoglobin levels and extreme signal levels in more than 5% of proteins measured with the modified aptamer platform are indicative of additional sample degradation. Of the 2496 samples that passed the QC metrics, 73 (n=37 derivation, n=36 validation) were deemed unfit for analysis because they were hemolyzed (n=22 derivation, n=26 validation) or had at least 5% of the proteins measured (n=15 derivation, n=10 validation) exceed an outlier threshold defined as the median ± the maximum of 6 median absolute deviations and 5 times the median.
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2 Table of 1130 Proteins Measured
eTable 1 (below): List of 1130 Proteins measured by Somalogic’s modified aptamer-based proteomic assay, Version 3. The 76 proteins that failed quality control metrics were excluded from the analysis are indicated in the fourth column.
Excluded from Protein Analyte UniProt ID Gene Analysis sPLA2-Iia
14-3-3 protein family -- --
14-3-3σ | Stratifin P31947 SFN
15-hydroxyprostaglandin P15428 HPGD dehydrogenase | 15-PGDH | HPG-1
3-hydroxyacyl-CoA dehydrogenase Q99714 HSD17B10 type-2|ABAD | ERAB
3-hydroxyisobutyrate dehydrogenase P31937 HIBADH
4-1BB | CD137 Q07011 TNFRSF9
4-1BB ligand | CD137L P41273 TNFSF9
6Ckine | CCL21 O00585 CCL21
6-Phosphogluconate dehydrogenase P52209 PGD
Acid ceramidase-like protein | N- acylethanolamine-hydrolyzing acid Q02083 NAAA
amidase | ASAHL
Acid phosphatase 1, soluble | Adipocyte acid phosphatase | LMW- P24666 ACP1
PTP
Acidic fibroblast growth factor | β- P05230 FGF1 endothelial cell growth factor
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Excluded from Protein Analyte UniProt ID Gene Analysis
Acidic leucine-rich nuclear Q92688 ANP32B phosphoprotein 32 family member B
Activated leukocyte cell adhesion Q13740 ALCAM molecule | CD166
Activated protein C P04070 PROC
Activin A | Inhibin β-A homodimer P08476 INHBA
Activin AB | Inhibin β-A:β-B P08476, P09529 INHBA INHBB heterodimer
Activin receptor-like kinase 1 | ALK-1 P37023 ACVRL1
Activin serine-threonine-protein P36896 ACVR1B kinase receptor type-1B | ALK-4
ADAM metallopeptidase domain 12 O43184 ADAM12
ADAM metallopeptidase domain 9 Q13443 ADAM9
ADAM metallopeptidase with Q9UHI8 ADAMTS1 thrombospondin motifs 1
ADAM metallopeptidase with Q76LX8 ADAMTS13 thrombospondin motifs 13
ADAM metallopeptidase with Q8TE58 ADAMTS15 thrombospondin motifs 15
ADAM metallopeptidase with thrombospondin motifs 4 | O75173 ADAMTS4
Aggrecanase 1
ADAM metallopeptidase with thrombospondin motifs 5 | Q9UNA0 ADAMTS5
Aggrecanase 2
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Excluded from Protein Analyte UniProt ID Gene Analysis Adaptor protein Crk-I P46108 CRK
Adenylate kinase 1 | Myokinase P00568 AK1
Adenylosuccinate lyase P30566 ADSL
Adiponectin Q15848 ADIPOQ Y
Adrenocorticotropic hormone P01189 POMC Y
Afamin P43652 AFM
Aflatoxin B1 aldehyde reductase O43488 AKR7A2
Aggrecan core protein P16112 ACAN
Agouti-related protein O00253 AGRP
AITRL | Activation-induced TNFR member Ligand | GITRL | Q9UNG2 TNFSF18 Glucocorticoid-induced TNF receptor ligand
Albumin P02768 ALB
Alcohol dehydrogenase (NADP+) | Aldo-keto reductase family 1 member P14550 AKR1A1
A1
Alkaline phosphatase, tissue- P05186 ALPL nonspecific isozyme
Alkaline sphingomyelinase Q6UWV6 ENPP7
Allograft inflammatory factor 1 P55008 AIF1
Aminoacylase-1 Q03154 ACY1
Amnionless Q9BXJ7 AMN Y
AMP kinase (α1β1γ1) Q13131, Q9Y478, P54619 PRKAA1 PRKAB1 PRKAG1
AMP kinase (α2β2γ1) P54646, O43741, P54619 PRKAA2 PRKAB2 PRKAG1
Amphiregulin P15514 AREG
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Excluded from Protein Analyte UniProt ID Gene Analysis Amyloid β A4 protein P05067 APP
Angiogenin P03950 ANG Y
Angiopoietin -related protein 4 Q9BY76 ANGPTL4
Angiopoietin-1 Q15389 ANGPT1
Angiopoietin-2 O15123 ANGPT2
Angiopoietin-4 Q9Y264 ANGPT4
Angiopoietin-like 3 Q9Y5C1 ANGPTL3
Angiostatin P00747 PLG
Angiotensin-converting enzyme 2 Q9BYF1 ACE2
Angiotensinogen P01019 AGT
Annexin A1 P04083 ANXA1
Annexin A2 | Annexin II P07355 ANXA2
Annexin A6 P08133 ANXA6
Anterior gradient protein 2 homolog O95994 AGR2
Anti-Mullerian hormone receptor, Q16671 AMHR2 type II
Antithrombin III P01008 SERPINC1
Apolipoprotein A-I P02647 APOA1 Y
Apolipoprotein B P04114 APOB
Apolipoprotein D P05090 APOD Y
Apolipoprotein E P02649 APOE Y
Apolipoprotein E (isoform E2) P02649 APOE Y
Apolipoprotein E (isoform E3) P02649 APOE Y
Apolipoprotein E (isoform E4) P02649 APOE Y
Apoptosis inhibitor 2 | C-IAP2 Q13489 BIRC3
Apoptosis regulator Bcl-2 P10415 BCL2
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Excluded from Protein Analyte UniProt ID Gene Analysis
Apoptosis regulator Bcl-X Q07817 BCL2L1
Arginase-1 P05089 ARG1
ARID domain-containing protein 3A Q99856 ARID3A
Artemin Q5T4W7 ARTN
Aryl hydrocarbon receptor-interacting O00170 AIP protein | XAP2
Arylsulfatase A P15289 ARSA
Arylsulfatase B P15848 ARSB
Asialoglycoprotein receptor 1 P07306 ASGR1
Aspartate aminotransferase | P17174 GOT1 Y Glutamic-oxaloacetic transaminase 1
ATP synthase β-subunit, mitochondrial P06576 ATP5B Y | ecto-ATPSβ
ATP-dependent DNA helicase II 70 kDa P12956 XRCC6 subunit | Ku70
Aurora kinase A O14965 AURKA
Aurora-related kinase 2 | Aurora B Q96GD4 AURKB
Azurocidin P20160 AZU1
B lymphocyte chemoattractant | BLC | O43927 CXCL13 BCA-1
B7 homolog 1 | CD274 Q9NZQ7 CD274
B7 homolog 2 | ICOS ligand O75144 ICOSLG
B7-2 | CD86 P42081 CD86
Bactericidal permeability-increasing P17213 BPI protein
Basal cell adhesion molecule P50895 BCAM Y
Basic fibroblast growth factor P09038 FGF2
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Excluded from Protein Analyte UniProt ID Gene Analysis
Basic fibroblast growth factor receptor P11362 FGFR1 1
BCAR3 breast cancer anti-estrogen O75815 BCAR3 resistance 3
B-cell maturation protein | BCMA Q02223 TNFRSF17
B-cell-activating factor | BAFF | BLyS | Q9Y275 TNFSF13B
B-cell-activating factor receptor | Q96RJ3 TNFRSF13C BAFF R
Bcl-2-related protein A1 Q16548 BCL2A1
Biglycan P21810 BGN
BMPER | BMP-binding endothelial Q8N8U9 BMPER regulator | Crossveinless-2
Bone marrow stromal cell antigen | Q10588 BST1 CD157
Bone morphogenetic protein receptor P36894 BMPR1A type IA | ALK-3
Bone morphogenetic protein type II Q13873 BMPR2 receptor
Bone morphogenetic protein-1 P13497 BMP1
Bone morphogenetic protein-10 O95393 BMP10 Y
Bone morphogenetic protein-14 | BMP-14 | Cartilage-Derived P43026 GDF5 Y Morphogenetic Protein-1 | CDMP-1
Bone morphogenetic protein-6 P22004 BMP6
Bone morphogenetic protein-7 P18075 BMP7
Bone sialoprotein 2 P21815 IBSP
Brain natriuretic peptide 32 | BNP-32 P16860 NPPB
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Excluded from Protein Analyte UniProt ID Gene Analysis
Brain-derived neurotrophic factor P23560 BDNF
Brain-specific serine protease 4 Q9GZN4 PRSS22
B-related factor 1 | Transcription Q92994 BRF1 factor IIIB 90 kDa subunit | TFIIIB90
Brevican Q96GW7 BCAN
C1-Esterase Inhibitor P05155 SERPING1
c-abl oncogene 1, non-receptor P00519 ABL1 tyrosine kinase
Cadherin-1 | E-cadherin (epithelial) P12830 CDH1
Cadherin-12 | BR-cadherin (brain) P55289 CDH12
Cadherin-15 | M-cadherin P55291 CDH15 (myotubule)
Cadherin-2 | N-cadherin (neuronal) P19022 CDH2
Cadherin-3 | P-cadherin (placental) P22223 CDH3
Cadherin-5 | VE-cadherin (vascular P33151 CDH5
Cadherin-6 | K-cadherin (kidney) P55285 CDH6
Calcineurin Q08209, P63098 PPP3CA PPP3R1
Calcineurin B α P63098 PPP3R1
Calcium-calmodulin-dependent Q14012 CAMK1 protein kinase I
Calcium-calmodulin-dependent Q8IU85 CAMK1D protein kinase ID
Calcium-calmodulin-dependent Q9UQM7 CAMK2A protein kinase II α
Calcium-calmodulin-dependent Q13554 CAMK2B protein kinase II β
Calcium-calmodulin-dependent Q13557 CAMK2D protein kinase II δ
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Excluded from Protein Analyte UniProt ID Gene Analysis
Calcium-calmodulin-dependent Q8N5S9 CAMKK1 protein kinase kinase 1 α
Calpain I P07384, P04632 CAPN1 CAPNS1
Calpastatin P20810 CAST
Calreticulin | Ro P27797 CALR
cAMP and cGMP phosphodiesterase Q9HCR9 PDE11A 11A | PDE11A
cAMP-dependent protein kinase P17612 PRKACA catalytic subunit α | PKA
cAMP-regulated phosphoprotein 19 P56211 ARPP19
cAMP-specific phosphodiesterase 4D | Q08499 PDE4D PDE4D
Carbohydrate sulfotransferase 15 Q7LFX5 CHST15
Carbohydrate sulfotransferase 2 Q9Y4C5 CHST2
Carbohydrate sulfotransferase 6 Q9GZX3 CHST6
Carbonic anhydrase I P00915 CA1
Carbonic anhydrase II P00918 CA2
Carbonic anhydrase III P07451 CA3
Carbonic anhydrase IV P22748 CA4 Y
Carbonic anhydrase IX Q16790 CA9
Carbonic anhydrase VI P23280 CA6
Carbonic anhydrase VII P43166 CA7
Carbonic anhydrase XIII Q8N1Q1 CA13
Carbonic anhydrase-related protein X Q9NS85 CA10
Carboxypeptidase E P16870 CPE
Cardiotrophin-1 Q16619 CTF1
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Excluded from Protein Analyte UniProt ID Gene Analysis
Carnosine dipeptidase 1 Q96KN2 CNDP1
Casein kinase II subunit α P68400 CSNK2A1 Y
Casein kinase II α1:β heterodimer P68400, P67870 CSNK2A1 CSNK2B
Casein kinase II α2:β heterodimer P19784, P67870 CSNK2A2 CSNK2B
Caspase-10 Q92851 CASP10
Caspase-2 P42575 CASP2
Caspase-3 P42574 CASP3
Catalase P04040 CAT
Cathepsin A P10619 CTSA
Cathepsin B P07858 CTSB
Cathepsin C P53634 CTSC
Cathepsin D P07339 CTSD
Cathepsin E P14091 CTSE
Cathepsin G P08311 CTSG
Cathepsin H P09668 CTSH
Cathepsin L2 | Cathepsin V O60911 CTSL2
Cathepsin S P25774 CTSS
Cathepsin Z/X/P Q9UBR2 CTSZ
CCL1 | CC chemokine 1 | I-309 P22362 CCL1
CCL18 | PARC |Macrophage P55774 CCL18 inflammatory protein 4
CCL28 Q9NRJ3 CCL28
CD109 Q6YHK3 CD109
CD200 | OX-2 membrane glycoprotein P41217 CD200
CD200 receptor 1 Q8TD46 CD200R1
CD22 | Siglec-2 P20273 CD22
CD23 | FCER2 P06734 FCER2
CD27 | TNFRSF7 P26842 CD27 Y
CD30 | TNFRSF8 | KI-1 P28908 TNFRSF8
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Excluded from Protein Analyte UniProt ID Gene Analysis
CD30 Ligand | TNFSF8 | CD153 P32971 TNFSF8
CD39 | Ecto-ATPDase 1 P49961 ENTPD1
CD40 ligand | TNFSF5 P29965 CD40LG
CD48 | SLAMF2 P09326 CD48
CD5 antigen-like O43866 CD5L
CD55 | Complement decay- P08174 CD55 accelerating factor | DAF
CD70 | TNFSF7 P32970 CD70
CD97 P48960 CD97
Cell adhesion oncogene-related CDO Q4KMG0 CDON
cGMP-binding cGMP-specific O76074 PDE5A phosphodiesterase | PDE5A
cGMP-inhibited cAMP Q14432 PDE3A phosphodiesterase 3A | PDE3A
Chemerin Q99969 RARRES2
Chitotriosidase-1 Q13231 CHIT1
Chordin-Like 1 Q9BU40 CHRDL1
Chromobox protein homolog 5 | HP1α P45973 CBX5
Chymase P23946 CMA1
Ciliary Neurotrophic Factor P26441 CNTF
Ciliary neurotrophic factor receptor α P26992 CNTFR
CKAP2 | Cytoskeleton-associated Q8WWK9 CKAP2 protein 2
CK-BB | Creatine kinase-BB P12277 CKB
CK-MB | Creatine kinase-MB P12277, P06732 CKB CKM
CK-MM | Creatine kinase-MM P06732 CKM
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Excluded from Protein Analyte UniProt ID Gene Analysis
Ck-β-8-1 | Macrophage inflammatory P55773 CCL23 protein 3 splice variant (aa 46-137)
Clusterin P10909 CLU Y CMRF-35A | CD300c Q08708 CD300C Y
Coactosin-like protein 1 | Novel Neurtrophin-1 | NNT-1 | B-Cell Q14019 COTL1 Stimulating Factor-3 | BCSF-3 | Cardiotrophin-like cytokine
Coagulation factor IX P00740 F9
Coagulation factor IXab P00740 F9
Coagulation factor V P12259 F5
Coagulation factor VII P08709 F7
Coagulation factor X P00742 F10 Y
Coagulation factor Xa P00742 F10
Coagulation factor XI P03951 F11 Y Cofilin-1 P23528 CFL1
Coiled-coil domain-containing protein Q76M96 CCDC80 80 | URB
Collagen α-1(VIII) chain P27658 COL8A1
Collagen α-1(XXIII) chain Q86Y22 COL23A1
Collectin Kidney 1 Q9BWP8 COLEC11
Collectin Placenta 1 Q5KU26 COLEC12
COMM domain containing 7 Q86VX2 COMMD7
Complement C1q P02745, P02746, P02747 C1QA C1QB C1QC
Complement C1q binding protein | Q07021 C1QBP Hyaluronan binding protein 1 | HABP1
Complement C1r P00736 C1R
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Excluded from Protein Analyte UniProt ID Gene Analysis Complement C1s P09871 C1S
Complement C2 P06681 C2
Complement C3 P01024 C3 Y
Complement C3a anaphylatoxin P01024 C3 Y
Complement C3a anaphylatoxin des P01024 C3 Arginine
Complement C3b P01024 C3 Y
Complement C3b, inactivated | iC3b P01024 C3 Y
Complement C3d P01024 C3
Complement C4 P0C0L4, P0C0L5 C4A C4B
Complement C4b P0C0L4, P0C0L5 C4A C4B
Complement C5 P01031 C5
Complement C5a P01031 C5 Y
Complement C5b,6 Complex P01031, P13671 C5 C6
Complement C6 P13671 C6
Complement C7 P10643 C7
Complement C8 P07357, P07358, P07360 C8A C8B C8G
Complement C9 P02748 C9
Complement factor B P00751 CFB
Complement factor D P00746 CFD
Complement factor H P08603 CFH
Complement factor H-related 5 Q9BXR6 CFHR5
Complement factor I P05156 CFI
Connective tissue growth factor | CCN2 | Hypertrophic chondrocyte- P29279 CTGF
specific protein 24 | HCS24
Connective-tissue activating peptide III P02775 PPBP | CTAP-III
Conserved dopamine neurotrophic Q49AH0 CDNF factor Contactin-1 Q12860 CNTN1
Contactin-2 Q02246 CNTN2
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Excluded from Protein Analyte UniProt ID Gene Analysis Contactin-4 Q8IWV2 CNTN4
Contactin-5 O94779 CNTN5
Copine-1 Q99829 CPNE1
Corticosteroid binding globulin P08185 SERPINA6
COX-2 | Prostaglandin H2 synthase 2 | P35354 PTGS2 Cyclooxygenase-2
C-reactive protein P02741 CRP
Cripto-1 P13385 TDGF1
CRTAM | cytotoxic and regulatory T O95727 CRTAM cell molecule
Cryptic protein P0CG37 CFC1
C-Src kinase | CSK P41240 CSK
C-type lectin domain family 1 member Q9P126 CLEC1B B | CLEC-2
Cutaneous T-cell-attracting chemokine Q9Y4X3 CCL27 | CTACK
Cyclin B1 P14635 CCNB1
Cyclin-dependent kinase 1:cyclin B P06493, P14635 CDC2 CCNB1 complex
Cyclin-dependent kinase 2:cyclin A P24941, P20248 CDK2 CCNA2 complex
Cyclin-dependent kinase 5:activator Q00535, Q15078 CDK5 CDK5R1 p35 complex
Cyclin-dependent kinase 8:cyclin C P49336, P24863 CDK8 CCNC complex
Cyclin-dependent kinase inhibitor p27 P46527 CDKN1B | p27kip1
Cyclophilin B | CypB P23284 PPIB Y Cystatin C P01034 CST3
Cystatin D P28325 CST5
Cystatin E/M Q15828 CST6
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Excluded from Protein Analyte UniProt ID Gene Analysis Cystatin F O76096 CST7
Cystatin S P01036 CST4
Cystatin SA P09228 CST2
Cystatin SN P01037 CST1
Cysteine-rich secretory protein 3 P54108 CRISP3
Cytochrome c P99999 CYCS
Cytochrome P450 3A4 P08684 CYP3A4
Cytokine-like factor 1:Cardiotrophin- O75462, Q9UBD9 CRLF1 CLCF1 like cytokine factor 1 Complex
Cytosolic non-specific dipeptidase 2 Q96KP4 CNDP2
Cytotoxic T-lymphocyte-4 P16410 CTLA4
dCTP pyrophosphatase 1 Q9H773 DCTPP1
D-dimer P02671, P02675, P02679 FGA FGB FGG
DEAD box RNA helicase 19B | DBP5 Q9UMR2 DDX19B
Death decoy receptor 3 | DcR3 O95407 TNFRSF6B
Death receptor 3 | DR3 Q93038 TNFRSF25
Death receptor 6 | DR6 O75509 TNFRSF21
Death-associated protein kinase 2 Q9UIK4 DAPK2
Decorin | Bone proteoglycan II P07585 DCN
Dectin-1 Q9BXN2 CLEC7A
Delta-like protein 1 O00548 DLL1
Dendritic cell-specific ICAM-3- Q9NNX6 CD209 grabbing nonintegrin 1 | DC-SIGN
Dendritic cell-specific ICAM-3- Q9H2X3 CLEC4M grabbing nonintegrin 2 | DC-SIGNR
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Excluded from Protein Analyte UniProt ID Gene Analysis
Dentin matrix protein 1 Q13316 DMP1
Dermatopontin Q07507 DPT Y
Desert hedgehog N-terminus O43323 DHH
Desmocollin-3 Q14574 DSC3
Desmoglein-1 Q02413 DSG1
Desmoglein-2 Q14126 DSG2
Dickkopf-related protein 1 O94907 DKK1
Dickkopf-related protein 3 Q9UBP4 DKK3
Dickkopf-related protein 4 Q9UBT3 DKK4
Dipeptidyl-peptidase II Q9UHL4 DPP7
Discoidin domain receptor 1 Q08345 DDR1
Discoidin domain receptor 2 Q16832 DDR2
DNA repair protein RAD51 homolog 1 Q06609 RAD51
DNA Topoisomerase I P11387 TOP1
DnaJ homolog subfamily C member 19 Q96DA6 DNAJC19
DNAX accessory molecule 1 | DNAM-1 Q15762 CD226
Dopa decarboxylase P20711 DDC
Dopamine responsive protein | DRG-1 Q9NP79 VTA1 | LIP5 | SBP1
Down-regulated in renal cell O95990 FAM107A carcinoma 1 | DRR1 | TU3A
Drebrin-like HIP-55 | Actin-binding Q9UJU6 DBNL protein 1 | mAbp1 | SH3P7
Drosophila delta homolog 4 Q9NR61 DLL4
Dual-specificity protein kinase 3 | O43781 DYRK3 Regulatory erythroid kinase | REDK
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Excluded from Protein Analyte UniProt ID Gene Analysis Dynactin subunit 2 Q13561 DCTN2
Dynein light chain 1 |DLC8 | LC8 P63167 DYNLL1
Dynein Roadblock light chain 1, RobI1 Q9NP97 DYNLRB1 | Km23
Ectodermal dysplasia receptor Q9UNE0 EDAR
Ectodysplasin-A, secreted form Q92838 EDA
Ectonucleoside triphosphate O75355 ENTPD3 diphosphohydrolase 3 | CD39L3
Ectonucleoside triphosphate O75356 ENTPD5 diphosphohydrolase 5 | CD39L4
EGF receptor | ErbB1 | HER1 P00533 EGFR
EGF-like module-containing mucin-like Q9UHX3 EMR2 receptor 2
EG-VEGF | PK1 | Endocrine-gland- derived vascular endothelial growth P58294 PROK1
factor
Elafin | Trappin-2 P19957 PI3
Elongation factor 1-β P24534 EEF1B2
Endocan Q9NQ30 ESM1
Endoglin | CD105 P17813 ENG
Endoplasmic reticulum Q9NZ08 ERAP1 aminopeptidase 1 | PILS | ARTS1
Endoplasmic reticulum resident P30040 ERP29 protein 29 | ERp29
Endostatin P39060 COL18A1
Endothelial cell-selective adhesion Q96AP7 ESAM molecule
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Excluded from Protein Analyte UniProt ID Gene Analysis
Endothelial-monocyte activating Q12904 AIMP1 polypeptide 2 | EMAP-2 | p43
Endothelin-converting enzyme 1 P42892 ECE1
Enterokinase | Enteropeptidase P98073 PRSS7
Eotaxin | CCL11 P51671 CCL11
Eotaxin-2 O00175 CCL24
EPH receptor A10 Q5JZY3 EPHA10
EPH receptor B2 P29323 EPHB2
EPH receptor B6 O15197 EPHB6
Ephrin type-A receptor 1 P21709 EPHA1
Ephrin type-A receptor 2 P29317 EPHA2
Ephrin type-A receptor 3 P29320 EPHA3
Ephrin type-A receptor 5 P54756 EPHA5
Ephrin type-B receptor 4 P54760 EPHB4 Y
Ephrin-A4 P52798 EFNA4
Ephrin-A5 P52803 EFNA5
Ephrin-B3 Q15768 EFNB3
Epidermal growth factor receptor Q9UBC2 EPS15L1 substrate 15-like 1 | Eps15R
Epiregulin O14944 EREG
Epithelial-derived neutrophil- P42830 CXCL5 activating protein 78 | ENA-78
ErbB2 | HER2 P04626 ERBB2
ErbB3 | HER3 P21860 ERBB3
ErbB3 binding protein Ebp1 Q9UQ80 PA2G4
ErbB4 | HER4 Q15303 ERBB4
Erythrocyte membrane protein 4.1 | P11171 EPB41 Y Protein 4.1R
© 2016 American Medical Association. All rights reserved.
Downloaded From: https://jamanetwork.com/ on 10/02/2021
Excluded from Protein Analyte UniProt ID Gene Analysis Erythropoietin P01588 EPO
Erythropoietin receptor P19235 EPOR
E-Selectin | CD62E | ELAM-1 P16581 SELE
Esterase D P10768 ESD
Estrogen receptor 1 | ERα P03372 ESR1
Ethylmalonic encephalopathy 1 O95571 ETHE1
Eukaryotic translation initiation factor P38919 EIF4A3 4A-III | DEAD-box protein 48 | DDX48
Eukaryotic translation initiation factor Q13542 EIF4EBP2 4E-binding protein 2
Eukaryotic translation initiation factor P55010 EIF5 5
Eukaryotic translation initiation factor P63241 EIF5A 5A
Eukaryotic translation initiation factor P78344 EIF4G2 G2 | p97 | DAP5.
Extracellular matrix metalloproteinase P35613 BSG Y inducer | EMMPRIN | Basigin | CD147
Extracellular matrix protein-1 Q16610 ECM1
FACT complex subunit SSRP1 Q08945 SSRP1
Fas ligand, soluble fragment | CD95L P48023 FASLG
Fatty acid binding protein, epidermal- Q01469 FABP5 Y type | E-FABP | C-FABP
Fatty acid binding protein, heart-type P05413 FABP3
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
Fc receptor-like protein 3 Q96P31 FCRL3
Ferritin P02794, P02792 FTH1 FTL
Fetuin B Q9UGM5 FETUB
Fibrinogen P02671, P02675, P02679 FGA FGB FGG
Fibrinogen γ chain dimer P02679 FGG
Fibroblast activation protein α Q12884 FAP
Fibroblast growth factor 10 | O15520 FGF10 Keratinocyte growth factor 2 | FGFA
Fibroblast growth factor 12 P61328 FGF12
Fibroblast growth factor 16 | FGFG O43320 FGF16
Fibroblast growth factor 17 | FGFH O60258 FGF17
Fibroblast growth factor 18 | zFGF5 | O76093 FGF18 FGFI
Fibroblast growth factor 19 | FGFJ O95750 FGF19
Fibroblast growth factor 20 | FGFK Q9NP95 FGF20
Fibroblast growth factor 23 Q9GZV9 FGF23
Fibroblast growth factor 4 P08620 FGF4
Fibroblast growth factor 5 P12034 FGF5
Fibroblast growth factor 6 | HST-2 P10767 FGF6
Fibroblast growth factor 7 | P21781 FGF7 Keratinocyte Growth Factor | KGF
Fibroblast growth factor 8 isoform A P55075 FGF8
Fibroblast growth factor 8 isoform B P55075 FGF8
Fibroblast growth factor 9 P31371 FGF9
© 2016 American Medical Association. All rights reserved.
Downloaded From: https://jamanetwork.com/ on 10/02/2021
Excluded from Protein Analyte UniProt ID Gene Analysis
Fibroblast growth factor receptor 2 P21802 FGFR2
Fibroblast growth factor receptor 3 P22607 FGFR3
Fibroblast growth factor receptor 4 P22455 FGFR4
Fibronectin P02751 FN1
Fibronectin leucine rich Q9NZU1 FLRT1 transmembrane 1
Fibronectin-1 fragment 3 P02751 FN1
Fibronectin-1 fragment 4 P02751 FN1
Ficolin-1 O00602 FCN1
Ficolin-2 Q15485 FCN2
Ficolin-3 O75636 FCN3
Fms-related tyrosine kinase 3 ligand | P49771 FLT3LG Flt3-Ligand
Focal adhesion kinase 1 | FAK1 Q05397 PTK2
Follicle stimulating hormone P01215, P01225 CGA FSHB
Follistatin P19883 FST
Follistatin-like 3 O95633 FSTL3
Fortilin | Translationally-controlled tumor protein | TCTP | Histamine- P13693 TPT1
releasing factor
Fractalkine | CX3CL-1 P78423 CX3CL1 Y
Frizzled-related protein 1, secreted Q8N474 SFRP1 Y
Frizzled-related protein 3, secreted Q92765 FRZB
Fucosyltransferase 3 P21217 FUT3
Fucosyltransferase 5 Q11128 FUT5
G protein-coupled receptor associated Q96D09 GPRASP2 sorting protein 2 | GASP-2 | WFIKKN
© 2016 American Medical Association. All rights reserved.
Downloaded From: https://jamanetwork.com/ on 10/02/2021
Excluded from Protein Analyte UniProt ID Gene Analysis Galectin-2 P05162 LGALS2
Galectin-3 P17931 LGALS3 Y
Galectin-3 binding protein | MAC-2BP Q08380 LGALS3BP
Galectin-4 P56470 LGALS4
Galectin-8 O00214 LGALS8
GDF-11/8 | Growth-differentiation O95390 GDF11 factor 11/8
GDF-2 | Growth-differentiation factor Q9UK05 GDF2 2 | BMP-9
GDF-9 | Growth-differentiation factor O60383 GDF9 9
GDNF family receptor α1 P56159 GFRA1
GDNF family receptor α2 O00451 GFRA2
GDNF family receptor α3 O60609 GFRA3
Gelsolin P06396 GSN
GITR | TNFRSF18 Q9Y5U5 TNFRSF18
Glial fibrillary acidic protein P14136 GFAP
Glucagon P01275 GCG
Glucocorticoid receptor P04150 NR3C1 Y
Glucokinase (hexokinase 4) regulator | Q14397 GCKR GCKR
Glucose phosphate isomerase | Neuroleukin | Autocrine motility P06744 GPI
factor
Glutathione S-transferase A3 | GSTA3- Q16772 GSTA3 3
Glutathione S-transferase Pi 1 P09211 GSTP1
Glyceraldehyde-3-phosphate P04406 GAPDH dehydrogenase
© 2016 American Medical Association. All rights reserved.
Downloaded From: https://jamanetwork.com/ on 10/02/2021
Excluded from Protein Analyte UniProt ID Gene Analysis
Glycogen synthase kinase-3 α/β P49840, P49841 GSK3A GSK3B
Glypican-2 Q8N158 GPC2
Glypican-3 P51654 GPC3
Glypican-5 P78333 GPC5
GP4 | CD36 | Platelet glycoprotein IV P16671 CD36
gp41 C34 peptide (HIV) Q70626 HIV env
G-protein coupled receptor 114 Q8IZF4 GPR114
GPT | Alanine aminotransaminase 1 | ALT | Gutamate pyruvate P24298 GPT
transaminanse
GPVI | Platelet glycoprotein VI Q9HCN6 GP6
Granulocyte chemotactic protein 2 | P80162 CXCL6 GCP-2 | CXCL6
Granulocyte colony-stimulating factor P09919 CSF3 Y | G-CSF
Granulocyte colony-stimulating factor Q99062 CSF3R receptor | CD114
Granulocyte-macrophage colony- P04141 CSF2 stimulating factor | GM-CSF
Granulysin P22749 GNLY
Granzyme A P12544 GZMA
Granzyme B P10144 GZMB
Granzyme H P20718 GZMH
GRAP2 | GRB2-related adaptor protein O75791 GRAP2 2 | Mona | Gads
Gremlin-1 O60565 GREM1
Growth arrest specific 1 P54826 GAS1
© 2016 American Medical Association. All rights reserved.
Downloaded From: https://jamanetwork.com/ on 10/02/2021
Excluded from Protein Analyte UniProt ID Gene Analysis
Growth hormone receptor P10912 GHR
Gro-α | CXCL1 | KC P09341 CXCL1
Gro-β/γ | CXCL2/3 | MIP2-α/β P19876, P19875 CXCL3 CXCL2
GTP-binding nuclear protein Ran | P62826 RAN ARA24 Haptoglobin P00738 HP
Heat shock cognate 70 kDa protein 8 P11142 HSPA8
Heme oxygenase 2 P30519 HMOX2
Hemofiltrate CC chemokine 1 | HCC-1 Q16627 CCL14 | CCL14
Hemoglobin P69905, P68871 HBA1 HBB
Hemojuvelin | RGMC Q6ZVN8 HFE2
Hemopexin P02790 HPX
Hemopoietic cell kinase P08631 HCK
Heparan-sulfate 6-O-sulfotransferase O60243 HS6ST1 1 Heparin cofactor II P05546 SERPIND1
Heparin-binding EGF-like growth Q99075 HBEGF factor
Hepatocyte growth factor P14210 HGF
Hepatocyte growth factor activator Q04756 HGFAC
Hepatocyte growth factor receptor | P08581 MET c-Met
Hepatoma-derived growth factor- Q7Z4V5 HDGFRP2 related protein 2 | HRP-2
Heterogeneous nuclear P22626 HNRNPA2B1 ribonucleoprotein A2/B1
Heterogeneous nuclear Q99729 HNRNPAB ribonucleoprotein AB
© 2016 American Medical Association. All rights reserved.
Downloaded From: https://jamanetwork.com/ on 10/02/2021
Excluded from Protein Analyte UniProt ID Gene Analysis
Heterogeneous nuclear P61978 HNRNPK ribonucleoprotein K | hnRNP K
Heterogeneous nuclear ribonucleoprotein Q | NSAP1 | GRY- O60506 SYNCRIP
RBP
High affinity cAMP-specific Q13946 PDE7A phosphodiesterase 7A | PDE7A
High affinity cAMP-specific O76083 PDE9A phosphodiesterase 9A | PDE9A
High temperature requirement serine O43464 HTRA2 peptidase A2 | OMI
High-mobility group box 1 | P09429 HMGB1 amphoterin
Histidine triad nucleotide binding P49773 HINT1 protein 1
Histidine-proline-rich glycoprotein | P04196 HRG Y HPRG
Histone acetyltransferase 1 O14929 HAT1
Histone acetyltransferase KAT6A | Q92794 KAT6A MOZ | MYST3
Histone deacetylase 8 Q9BY41 HDAC8
Histone H1.2 P16403 HIST1H1C
Histone H2A.z P0C0S5 H2AFZ
Histone H3-K9 methyltransferase 3 Q96KQ7 EHMT2
HMG-CoA reductase P04035 HMGCR
Homeobox transcription factor Nanog Q9H9S0 NANOG
© 2016 American Medical Association. All rights reserved.
Downloaded From: https://jamanetwork.com/ on 10/02/2021
Excluded from Protein Analyte UniProt ID Gene Analysis
Homeodomain-interacting protein Q9H422 HIPK3 kinase 3 | YAK1
HSP 90α/β P07900, P08238 HSP90AA1 HSP90AB1
Hsp40 | HDJ1 P25685 DNAJB1
Hsp60 P10809 HSPD1
Hsp70 P08107 HSPA1A
Hsp90 co-chaperone Cdc37 Q16543 CDC37
Human chorionic gonadotropin P01215, P01233 CGA CGB
HVEM | TNFRSF14 Q92956 TNFRSF14
Hyaluronan and proteoglycan link P10915 HAPLN1 protein 1
Hydroxysteroid 17-β-dehydrogenase 1 P14061 HSD17B1
Iduronate 2-sulfatase P22304 IDS
IgA Fc receptor | CD89 P24071 FCAR
IgG Fc receptor I | CD64 P12314 FCGR1A
Immunoglobulin D P01880 IGHD IGK@ IGL@
Immunoglobulin E P01854 IGHE IGK@ IGL@
IGHG1 IGHG2 IGHG3 IGHG4 Immunoglobulin G P01857 Y IGK@ IGL@
Immunoglobulin G Fc region receptor O75015 FCGR3B III-B, low affinity | D16b
Immunoglobulin M P01871 IGHM IGJ IGK@ IGL@
IMP (inosine 5'-monophosphate) P20839 IMPDH1 dehydrogenase 1 | RP10
IMP (inosine 5'-monophosphate) P12268 IMPDH2 dehydrogenase 2
Importin β1 | Karyopherin β-1 | Q14974 KPNB1 Nuclear factor P97
Inducible T-cell co-stimulator Q9Y6W8 ICOS
Inferferon-α2 P01563 IFNA2
© 2016 American Medical Association. All rights reserved.
Downloaded From: https://jamanetwork.com/ on 10/02/2021
Excluded from Protein Analyte UniProt ID Gene Analysis Inferferon-γ P01579 IFNG
Inferferon-γ receptor 1 P15260 IFNGR1
Inferferon-λ 1 Q8IU54 IL29
Inferferon-λ 2 Q8IZJ0 IL28A
Inhibitor of growth 1 Q9UK53 ING1 Y
Inorganic pyrophosphatase Q15181 PPA1 Y
Insulin P01308 INS
Insulin receptor | IR | CD220 P06213 INSR
Insulin-degrading enzyme | Insulysin P14735 IDE
Insulin-like growth factor I P05019 IGF1
Insulin-like growth factor I receptor P08069 IGF1R
Insulin-like growth factor II receptor P11717 IGF2R
Insulin-like growth factor-binding P08833 IGFBP1 protein 1
Insulin-like growth factor-binding P18065 IGFBP2 protein 2
Insulin-like growth factor-binding P17936 IGFBP3 Y protein 3
Insulin-like growth factor-binding P22692 IGFBP4 Y protein 4
Insulin-like growth factor-binding P24593 IGFBP5 protein 5
Insulin-like growth factor-binding P24592 IGFBP6 protein 6
Insulin-like growth factor-binding Q16270 IGFBP7 protein 7
Integrin α-I: β-1 complex | VLA-1 P56199, P05556 ITGA1 ITGB1
© 2016 American Medical Association. All rights reserved.
Downloaded From: https://jamanetwork.com/ on 10/02/2021
Excluded from Protein Analyte UniProt ID Gene Analysis
Integrin α-IIb: β-3 complex | Platelet P08514, P05106 ITGA2B ITGB3 Membrane Glycoproteins gpIIbIIIa
Integrin α-V: β-5 complex | P06756, P18084 ITGAV ITGB5 Fibronectin Receptor
Intercellular adhesion molecule 1 | P05362 ICAM1 CD54
Intercellular adhesion molecule 2 | P13598 ICAM2 CD102
Intercellular adhesion molecule 3 | P32942 ICAM3 CD50
Intercellular adhesion molecule 5 Q9UMF0 ICAM5
Interferon-γ induced protein 10 | IP- P02778 CXCL10 10
Interferon-γ-inducible protein-9 | I- O14625 CXCL11 TAC
Interleukin-1 receptor 1 P14778 IL1R1
Interleukin-1 receptor accessory Q9NPH3 IL1RAP protein | IL-1 RAcP | IL1 R3
Interleukin-1 receptor accessory Q9NP60 IL1RAPL2 protein-like 2 | IL-1 sR9
Interleukin-1 receptor-like 1 | ST2 | Q01638 IL1RL1 Interleukin-1 receptor 4
Interleukin-1 receptor-like 2 | IL-1Rrp2 Q9HB29 IL1RL2
Interleukin-10 P22301 IL10
Interleukin-10 receptor β Q08334 IL10RB
Interleukin-11 P20809 IL11
© 2016 American Medical Association. All rights reserved.
Downloaded From: https://jamanetwork.com/ on 10/02/2021
Excluded from Protein Analyte UniProt ID Gene Analysis
Interleukin-11 receptor α Q14626 IL11RA
Interleukin-12 P29459, P29460 IL12A IL12B
Interleukin-12 receptor β1 P42701 IL12RB1
Interleukin-12 receptor β2 Q99665 IL12RB2
Interleukin-13 P35225 IL13
Interleukin-13 receptor α1 P78552 IL13RA1
Interleukin-15 receptor α Q13261 IL15RA
Interleukin-16 Q14005 IL16
Interleukin-17 receptor A Q96F46 IL17RA
Interleukin-17 receptor B Q9NRM6 IL17RB
Interleukin-17 receptor C Q8NAC3 IL17RC
Interleukin-17 receptor D | SEF Q8NFM7 IL17RD
Interleukin-17A Q16552 IL17A
Interleukin-17B | IL20 | NIRF Q9UHF5 IL17B
Interleukin-17D | IL-27 Q8TAD2 IL17D
Interleukin-17E Q9H293 IL25
Interleukin-17F Q96PD4 IL17F
Interleukin-18 binding protein O95998 IL18BP
Interleukin-18 receptor α Q13478 IL18R1
Interleukin-18 receptor β O95256 IL18RAP
Interleukin-19 Q9UHD0 IL19
Interleukin-1α | IL-1F1 P01583 IL1A
Interleukin-1β | IL-1F2 P01584 IL1B Y
Interleukin-2 P60568 IL2
Interleukin-2 receptor α chain P01589 IL2RA
© 2016 American Medical Association. All rights reserved.
Downloaded From: https://jamanetwork.com/ on 10/02/2021
Excluded from Protein Analyte UniProt ID Gene Analysis
Interleukin-2 receptor γ chain | P31785 IL2RG Cytokine receptor common chain
Interleukin-20 Q9NYY1 IL20
Interleukin-20 receptor subunit a Q9UHF4 IL20RA
Interleukin-22 Q9GZX6 IL22
Interleukin-22 receptor α-1 Q8N6P7 IL22RA1
Interleukin-22 receptor subunit α2 | Q969J5 IL22RA2 IL-22BP
Interleukin-23 P29460, Q9NPF7 IL12B IL23A
Interleukin-23 receptor Q5VWK5 IL23R
Interleukin-24 Q13007 IL24
Interleukin-27 Q8NEV9 IL27
Interleukin-27 receptor subunit α | Q6UWB1 IL27RA TCCR | WSX-1
Interleukin-3 P08700 IL3
Interleukin-3 receptor α P26951 IL3RA
Interleukin-34 Q6ZMJ4 IL34
Interleukin-37 Q9NZH6 IL1F7
Interleukin-4 P05112 IL4
Interleukin-4 receptor α chain P24394 IL4R
Interleukin-5 P05113 IL5 Y
Interleukin-5 receptor α Q01344 IL5RA
Interleukin-6 P05231 IL6
Interleukin-6 receptor subunit α P08887 IL6R
Interleukin-6 receptor subunit β | P40189 IL6ST gp130
Interleukin-7 P13232 IL7
Interleukin-7 receptor subunit α P16871 IL7R
Interleukin-8 | CXCL8 P10145 IL8
© 2016 American Medical Association. All rights reserved.
Downloaded From: https://jamanetwork.com/ on 10/02/2021
Excluded from Protein Analyte UniProt ID Gene Analysis
Inter-α-trypsin inhibitor heavy chain Q14624 ITIH4 H4 | ITI-H4
Jagged-1 P78504 JAG1
Jagged-2 Q9Y219 JAG2
Janus kinase 2 O60674 JAK2
Junctional adhesion molecule B | JAM- P57087 JAM2 2 | VE-JAM
Junctional adhesion molecule C | JAM- Q9BX67 JAM3 3
Junctional adhesion molecule-like Q86YT9 AMICA1
Kallikrein 11 Q9UBX7 KLK11
Kallikrein 12 Q9UKR0 KLK12
Kallikrein 13 Q9UKR3 KLK13
Kallikrein 14 Q9P0G3 KLK14
Kallikrein 3 | PSA P07288 KLK3
Kallikrein 4 | Prostase Q9Y5K2 KLK4
Kallikrein 5 Q9Y337 KLK5
Kallikrein 6 | Neurosin Q92876 KLK6
Kallikrein 7 P49862 KLK7
Kallikrein 8 | Neuropsin O60259 KLK8
Kallistatin P29622 SERPINA4
Karyopherin α 2 | Importin α1 P52292 KPNA2
Keratin 18 P05783 KRT18
Killer cell immunoglobulin-like Q99706 KIR2DL4 receptor 2DL4
Killer cell immunoglobulin-like P43630 KIR3DL2 receptor 3DL2
Killer cell immunoglobulin-like Q14943 KIR3DS1 receptor 3DS1
Killer cell lectin-like receptor subfamily Q9NZS2 KLRF1 F, member 1 | NKp80
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
Kinesin family member 23 | CHO1 | Q02241 KIF23 MKLP-1
Kininogen-1, HMW, Single chain P01042 KNG1
Kirrel3 | NEPH2 Q8IZU9 KIRREL3
KRAS P01116 KRAS
Kremen protein 2 Q8NCW0 KREMEN2
Kunitz-type protease inhibitor 1 | Hepatocyte growth factor activator O43278 SPINT1
inhibitor | HAI inhibitor type 1
Kunitz-type protease inhibitor 2A | O43291 SPINT2 HAI-2 Kynureninase Q16719 KYNU
Lactate dehydrogenase 1 (heart) P07195 LDHB
Lactoferrin P02788 LTF
Lactoperoxidase P22079 LPO
Lamin-B1 P20700 LMNB1
Laminin P25391, P07942, P11047 LAMA1 LAMB1 LAMC1 Y
Laminin receptor | p40 ribosomal P08865 RPSA protein SA
Langerin Q9UJ71 CD207
Layilin Q6UX15 LAYN
LD78-β | CCL3L1 P16619 CCL3L1
LEAP-1 | Hepcidin P81172 HAMP
Legumain | Asparaginyl Q99538 LGMN endopeptidase
Leptin | Obesity protein (OB) P41159 LEP
Leptin receptor P48357 LEPR
Leucine carboxyl methyltransferase 1 Q9UIC8 LCMT1
Leucine-rich repeat transmembrane Q86UE6 LRRTM1 neuronal protein 1
© 2016 American Medical Association. All rights reserved.
Downloaded From: https://jamanetwork.com/ on 10/02/2021
Excluded from Protein Analyte UniProt ID Gene Analysis
Leucine-rich repeat transmembrane Q86VH5 LRRTM3 neuronal protein 3
Leucine-rich repeats and Ig-like Q6UXM1 LRIG3 domains protein 3
Leukemia inhibitory factor receptor P42702 LIFR extracellular domain
Leukocyte immunoglobulin-like receptor subfamily B member 1 | Q8NHL6 LILRB1
CD85j | ILT-2
Leukocyte immunoglobulin-like receptor subfamily B member 2 | Q8N423 LILRB2
CD85d | ILT-4
Leukotriene A-4 hydrolase P09960 LTA4H
LIGHT | TNFSF14 O43557 TNFSF14
Limbic system-associated membrane Q13449 LSAMP protein | LAMP
Lipocalin 2 | NGAL P80188 LCN2 Y
Lipopolysaccharide-binding protein P18428 LBP
Liver-expressed chemokine | HCC-4 O15467 CCL16
Livin | Baculoviral IAP repeat Q96CA5 BIRC7 containing 7 | ML-IAP
Low affinity immunoglobulin gamma P12318, P31994 FCGR2A FCGR2B Fc region receptor II-a/b
LRP8 | Apolipoprotein E receptor 2 Q14114 LRP8
L-Selectin | CD62L P14151 SELL
Luteinizing hormone P01215, P01229 CGA LHB
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
Lymphatic vessel endothelial Q9Y5Y7 LYVE1 hyaluronic acid receptor 1
Lymphocyte activation gene-1 | LAG-1 Q8NHW4 CCL4L1 | CCL4L1
Lymphocyte antigen 86 | Myeloid O95711 LY86 differentiation 1 | MD-1
Lymphocyte-activation gene 3 | LAG-3 P18627 LAG3
Lymphocyte-specific protein tyrosine P06239 LCK kinase Lck
Lymphotactin P47992 XCL1
Lymphotoxin α1:β2 P01374, Q06643 LTA LTB
Lymphotoxin α2:β1 P01374, Q06643 LTA LTB
Lymphotoxin β receptor P36941 LTBR
Lyn kinase | Lyn A P07948 LYN
Lyn kinase | Lyn B P07948 LYN
Lysosome membrane protein 2 | Q14108 SCARB2 LIMPII | SCARB2
Lysozyme P61626 LYZ
M2-pyruvate kinase P14618 PKM2
Macrophage colony-stimulating factor P09603 CSF1 1 | M-CSF
Macrophage colony-stimulating factor P07333 CSF1R 1 receptor | M-CSF R
Macrophage inflammatory protein 1 α P10147 CCL3 | MIP-1a
Macrophage inflammatory protein 3 α P78556 CCL20 | MIP-3a
Macrophage inflammatory protein 3 β Q99731 CCL19 | MIP-3b
© 2016 American Medical Association. All rights reserved.
Downloaded From: https://jamanetwork.com/ on 10/02/2021
Excluded from Protein Analyte UniProt ID Gene Analysis
Macrophage inflammatory protein 5 | Q16663 CCL15 Y MIP-1 delta | Leukotactin-1 | Lkn-1
Macrophage mannose receptor P22897 MRC1
Macrophage mannose receptor 2 | Q9UBG0 MRC2 uPARAP | Endo180
Macrophage scavenger receptor | SR- P21757 MSR1 A
Macrophage stimulatory protein | P26927 MST1 MSP
Macrophage stimulatory protein Q04912 MST1R receptor | RON
Macrophage-capping protein | Actin- P40121 CAPG capping protein CapG
Macrophage-derived chemokine | O00626 CCL22 MDC
Malate dehydrogenase, cytoplasmic P40925 MDH1
Mammaglobin B | Secretoglobin 2A1 O75556 SCGB2A1
Mannan-binding lectin serine P48740 MASP1 peptidase 1 | MASP3 catalytic domain
Mannose-binding protein C | MBL P11226 MBL2
MAPK 1 | MAP kinase 2 | ERK-2 |p42- P28482 MAPK1 MAPK
MAPK 11 | MAP kinase p38 β | SAPK2 Q15759 MAPK11
MAPK 12 | p38 γ P53778 MAPK12
MAPK 13 | p38 δ O15264 MAPK13
MAPK 14 | SAP KINASE 2A Q16539 MAPK14
MAPK 3 | ERK-1 | p44-MAPK P27361 MAPK3
MAPK 8 | JNK1 P45983 MAPK8
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
MAPK kinase 1 | MEK1 Q02750 MAP2K1
MAPK kinase 2 | MEK2 P36507 MAP2K2
MAPK kinase 4 | SAPK-ERK kinase 1 | P45985 MAP2K4 JNKK
MAPK-activated protein kinase 2 P49137 MAPKAPK2
MAPK-activated protein kinase 3 Q16644 MAPKAPK3
MAPK-activated protein kinase 5 | Q8IW41 MAPKAPK5 PRAK
Marapsin | pancreasin Q9BQR3 PRSS27 Y
Matrilin-2 O00339 MATN2
Matrilin-3 O15232 MATN3
Matrix extracellular Q9NQ76 MEPE phosphoglycoprotein | OF45
MDM2 ubiquitin ligase Q00987 MDM2
Mediator complex subunit 1 | MED1 | Q15648 MED1 TRAP220
Megakaryocyte-associated tyrosine- P42679 MATK protein kinase | Hyl | CTK
Melanoma inhibitory activity | Cartilage-derived retinoic acid- Q16674 MIA
sensitive protein | CD-RAP
Membrane frizzled-related protein | Q9BY79 MFRP MFRP
Mesothelin Q13421 MSLN
Methionine aminopeptidase 1 P53582 METAP1
Methionine aminopeptidase 2 P50579 METAP2
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
Methyl-CpG-binding domain protein 4 O95243 MBD4 | Base excision repair enzyme MED1
MHC class I polypeptide-related Q29983 MICA sequence A
MHC class I polypeptide-related Q29980 MICB sequence B
Microtubule-associated protein tau P10636 MAPT
Midkine P21741 MDK
MIF | macrophage migration P14174 MIF inhibitory factor
Milk fat globule-EGF factor 8 Q08431 MFGE8
Mitochondrial glutamate carrier 2 Q9H1K4 SLC25A18
Mitogen-activated protein kinase 9 | P45984 MAPK9 Y JNK2 α2
MMP-1 | Matrix metalloproteinase 1 | P03956 MMP1 Collagenase 1
MMP-10 | Matrix metalloproteinase P09238 MMP10 10 | Stromelysin 2
MMP-12 | Matrix metalloproteinase P39900 MMP12 12 | Macrophage metalloelastase
MMP-13 | Matrix metalloproteinase P45452 MMP13 13 | Collagenase 3
MMP-14 | Matrix metalloproteinase 14 | Membrane-type matrix P50281 MMP14
metalloproteinase 1
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
MMP-16 | Matrix metalloproteinase 16 | Membrane-type matrix P51512 MMP16
metalloproteinase 3
MMP-17 | Matrix metalloproteinase 17 | Membrane-type matrix Q9ULZ9 MMP17
metalloproteinase 4
MMP-2 | Matrix metalloproteinase 2 | P08253 MMP2 Gelatinase A
MMP-3 | Matrix metalloproteinase 3 | P08254 MMP3 Stromelysin 1
MMP-7 | Matrix metalloproteinase 7 | P09237 MMP7 Matrilysin
MMP-8 | Matrix metalloproteinase 8 | P22894 MMP8 Neutrophil collagenase
MMP-9 | Matrix metalloproteinase 9 | P14780 MMP9 Gelatinase B
Moesin P26038 MSN
Monocyte chemoattractant protein 1 P13500 CCL2 | MCP-1
Monocyte chemoattractant protein 2 P80075 CCL8 | MCP-2
Monocyte chemoattractant protein 3 P80098 CCL7 | MCP-3
Monocyte chemoattractant protein 4 Q99616 CCL13 | MCP-4
MPIF-1 | Myeloid progenitor P55773 CCL23 inhibitory factor 1
Muellerian-inhibiting factor | MIS P03971 AMH
Myeloperoxidase P05164 MPO
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis Myoglobin P02144 MB
Myotonic dystrophy protein kinase- Q9Y5S2 CDC42BPB like β | MRCKB
N-acetyl-D-glucosamine kinase Q9UJ70 NAGK
N-acetylglucosamine-6-sulfatase P15586 GNS Y
NADPH-P450 Oxidoreductase P16435 POR
Nascent polypeptide-associated Q13765 NACA Y complex α subunit | αNAC
Natural cytotoxicity triggering O76036 NCR1 receptor 1 | NKp46
Natural cytotoxicity triggering O95944 NCR2 receptor 2 | NKp44
Natural cytotoxicity triggering O14931 NCR3 receptor 3 | NKp30
Natural killer group 2 member D | P26718 KLRK1 NKG2D
NCC27 | Chloride intracellular channel O00299 CLIC1 protein 1
NCK-α SH2-SH3 adaptor protein P16333 NCK1
Nectin-like protein 1 | IGSF4B | NECL1 Q8N126 CADM3 | TSLL1 | SynCAM3
Nectin-like protein 2 | IGSF4 | TSLC1 | Q9BY67 CADM1 SynCAM1
Nephroblastoma overexpressed gene P48745 NOV | NovH | CCN3 | IGFBP9
Neprilysin-2 Q495T6 MMEL1
N-ethylmaleimide-sensitive factor P54920 NAPA (NSF) attachment protein α | αSNAP
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
Netrin receptor UNC5H3 O95185 UNC5C
Netrin receptor UNC5H4 Q6UXZ4 UNC5D
Netrin-4 Q9HB63 NTN4
Neural cell adhesion molecule 1 P13591 NCAM1 (CD56), 120 kDa isoform
Neural cell adhesion molecule L1 P32004 L1CAM
Neural cell adhesion molecule L1-like O00533 CHL1 protein | L1CAM-2
Neuregulin-1 | Heregulin Q02297 NRG1
Neurexin-1-β P58400 NRXN1
Neurexin-3-β Q9HDB5 NRXN3
Neurexophilin-1 P58417 NXPH1
Neuroblastoma suppressor of P41271 NBL1 tumorigenicity 1 | DAN
Neuroligin 4, X-linked Q8N0W4 NLGN4X
Neuropilin-1 O14786 NRP1
Neurotrophic tyrosine kinase receptor P04629 NTRK1 type 1 | TrkA
Neurotrophic tyrosine kinase receptor Q16620 NTRK2 type 2 | TrkB
Neurotrophic tyrosine kinase receptor Q16288 NTRK3 type 3 | TrkC
Neurotrophin-3 | NT-3 P20783 NTF3
Neurotrophin-4 | NT-4 | P34130 NTF4 Neurotrophin-5 | NT-5
Neutral ceramidase Q9NR71 ASAH2
Neutrophil elastase | Leukocyte P08246 ELANE elastase | Elastase 2 | PMN-elastase
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
Neutrophil-activating peptide 2 | NAP- P02775 PPBP 2 | CXCL7
Nicotinamide phosphoribosyltransferase | Pre-B-cell P43490 NAMPT
colony-enhancing factor 1 | Visfatin
Nidogen | Entactin P14543 NID1
Nidogen-2 Q14112 NID2
N-myristoyltransferase 1 P30419 NMT1
Noggin Q13253 NOG Y
Nogo receptor | reticulon 4 receptor Q9BZR6 RTN4R
Non-pancreatic secretory P14555 PLA2G2A phospholipase A2 |
Notch 1 P46531 NOTCH1
Notch 2 Q04721 NOTCH2
Notch 3 Q9UM47 NOTCH3
NR1D1 | nuclear receptor subfamily 1, P20393 NR1D1 group D, member 1 | Rev-erbA-α
NRCAM | neuronal cell adhesion Q92823 NRCAM molecule
Nuclear oncogene protein SET | TAF-Iβ Q01105 SET Y | I-2PP2A
Nucleoside diphosphate kinase A | P15531 NME1 Y Nm23-H1
Nucleoside diphosphate kinase B | P22392 NME2 Nm23-H2
NudC domain-containing protein 3 | Q8IVD9 NUDCD3 NudCL
Olfactomedin-4 | hGC-1 | GW112 Q6UX06 OLFM4 Y
Oncostatin M P13725 OSM
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
Opioid-binding cell adhesion molecule Q14982 OPCML | OBCAM
Osteoactivin | GPNMB Q14956 GPNMB
Osteomodulin | Osteoadherin Q99983 OMD
Osteonectin P09486 SPARC
Osteoprotegerin | OPG O00300 TNFRSF11B Y
Osteoprotegerin ligand | TRANCE | O14788 TNFSF11 sRANKL
Ovarian cancer immunoreactive antigen domain containing 1 | OCIA Q9NX40 OCIAD1
domain containing 1
OX40 Ligand | Tumor necrosis factor P23510 TNFSF4 ligand superfamily member 4
Oxidized low-density lipoprotein P78380 OLR1 receptor 1 | LOX-1
OXO | CD134 P43489 TNFRSF4
p21-activated kinase 3 O75914 PAK3 Y
p21-activated kinase 6 Q9NQU5 PAK6
p21-activated kinase 7 | KIAA1264 Q9P286 PAK7
p97 cofactor p47 Q9UNZ2 NSFL1C
PAFAH β subunit | Platelet-activating P68402 PAFAH1B2 factor acetylhydrolase IB subunit β
Pancreatic hormone P01298 PPY
Paraoxonase 1 P27169 PON1
Parathyroid hormone P01270 PTH
Parathyroid hormone-related protein P12272 PTHLH | PTHrP
© 2016 American Medical Association. All rights reserved.
Downloaded From: https://jamanetwork.com/ on 10/02/2021
Excluded from Protein Analyte UniProt ID Gene Analysis
PARK7 | Parkinson protein 7 | DJ-1 Q99497 PARK7
PCSK9 | Proprotein convertase Q8NBP7 PCSK9 subtilisin kexin type 9
PDK-1 | 3-phosphoinositide- O15530 PDPK1 dependent protein kinase 1
Peptide YY P10082 PYY
Peptidoglycan recognition protein, O75594 PGLYRP1 short | PGRP-S
Peptidylprolyl isomerase A P62937 PPIA Y |Cyclophilin A
Peptidylprolyl isomerase D | Q08752 PPID Cyclophilin D | Cyclophilin 40
Peptidylprolyl isomerase E | Q9UNP9 PPIE Cyclophilin E
Peptidylprolyl isomerase F (Cyclophilin P30405 PPIF Y F)
Periostin | Osteoblast-specific factor 2 Q15063 POSTN | OSF-2
Peroxiredoxin-1 Q06830 PRDX1
Peroxiredoxin-5 P30044 PRDX5
Peroxiredoxin-6 | AOP2 | 1-cysPrx P30041 PRDX6
Persephin O60542 PSPN
Pescadillo O00541 PES1
Phosphatase and tensin homolog P60484 PTEN
Phosphatidylethanolamine-binding P30086 PEBP1 protein 1 | HCNP | RKIP
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
Phosphatidylinositol-4,5-bisphosphate P48736 PIK3CG 3-kinase catalytic subunit γ | p110 γ
Phosphodiesterase 2A, cGMP- O00408 PDE2A stimulated
Phosphoglycerate kinase 1 P00558 PGK1
Phosphoglycerate mutase 1 P18669 PGAM1 Y
Phosphoinositide-3-kinase catalytic α polypeptide:regulatory subunit 1α P42336, P27986 PIK3CA PIK3R1
complex | p110 α:p85 α
Phospholipase A2, Group IB | type I P04054 PLA2G1B pancreatic sPLA2
Phospholipase A2, Group IIE Q9NZK7 PLA2G2E
Phospholipase A2, Group V P39877 PLA2G5
Phospholipase A2, Group X O15496 PLA2G10
Phospholipase C-II | PLCγ1 P19174 PLCG1
Pituitary adenylate cyclase-activating P18509 ADCYAP1 polypeptide 27 | PACAP-27
Pituitary adenylate cyclase-activating P18509 ADCYAP1 polypeptide 38 | PACAP-38
Placenta growth factor | PlGF P49763 PGF
Plasmin P00747 PLG
Plasminogen P00747 PLG
Plasminogen activator inhibitor 1 P05121 SERPINE1
Platelet endothelial cell adhesion P16284 PECAM1 molecule | CD31
Platelet factor 4 P02776 PF4 Y
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
Platelet glycoprotein Ib α P07359 GP1BA
Platelet-activating factor Q13093 PLA2G7 acetylhydrolase | PAF-AH | Lp-PLA2
Platelet-derived growth factor A chain P04085 PDGFA homodimer
Platelet-derived growth factor B chain P01127 PDGFB homodimer
Platelet-derived growth factor C chain Q9NRA1 PDGFC homodimer
Platelet-derived growth factor P09619 PDGFRB receptor β-type
Pleiotrophin P21246 PTN Y Plexin C1 O60486 PLXNC1
Polymeric immunoglobulin receptor P01833 PIGR
Prefoldin subunit 5 | MM-1 Q99471 PFDN5
Pregnancy-associated plasma protein- Q13219 PAPPA A | Pappalysin-1 | DIPLA1
Prekallikrein P03952 KLKB1
Programmed cell death 1 ligand 2 | Q9BQ51 PDCD1LG2 PD-L2 | B7-DC
Progranulin P28799 GRN
Prolactin P01236 PRL
Prolactin receptor P16471 PRLR
Proliferating cell nuclear antigen | P12004 PCNA PCNA
Properdin | Factor P P27918 CFP
Proprotein convertase 7 Q16549 PCSK7
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
Prostate-specific membrane antigen | Q04609 FOLH1 PSMA
Protease nexin 1 | PN1 P07093 SERPINE2
Proteasome activator complex subunit Q06323 PSME1 1 | PA28 α
Proteasome activator complex subunit P61289 PSME3 3 | REG-γ
Proteasome subunit p40 | MOV34 | P51665 PSMD7 Mov34 protein homolog
Proteasome subunit α type-1 P25786 PSMA1
Proteasome subunit α type-2 | α-type P25787 PSMA2 HC3 Proteasome subunit α type-6 | PROS- P60900 PSMA6 27 Protein C P04070 PROC
Protein C Inhibitor P05154 SERPINA5 Y
Protein disulfide isomerase A3 | P30101 PDIA3 ERp57 | GRp58 | ER-60
Protein disulfide-isomerase P07237 P4HB
Protein E7 (Human Papillomavirus P03129 HPV18 E7 Type 16)
Protein E7 (Human Papillomavirus P06788 HPV16 E7 Type 18)
Protein FAM107B Q9H098 FAM107B
Protein kinase B α/β/γ (RAC family) Family
Protein kinase C α P17252 PRKCA
Protein kinase C β type (splice variant P05771 PRKCB β-II)
Protein kinase C γ P05129 PRKCG Y Protein kinase C δ Q05655 PRKCD
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
Protein kinase C ζ | PKCzeta Q05513 PRKCZ
Protein kinase C θ Q04759 PRKCQ
Protein kinase C ι P41743 PRKCI
Protein lin-7 homolog B | MALS-2 | Q9HAP6 LIN7B Veli-2
Protein Rev (HIV) P18093 HIV rev
Protein S P07225 PROS1
Proteinase-3 | PR3 P24158 PRTN3
Prothrombin | Coagulation factor II P00734 F2
Proto-oncogene serine/threonine- P11309 PIM1 protein kinase Pim-1
Proto-oncogene tyrosine-protein P09769 FGR kinase Fgr
Proto-oncogene tyrosine-protein P06241 FYN kinase Fyn | FYNT
Proto-oncogene tyrosine-protein P07949 RET kinase receptor Ret
Proto-oncogene tyrosine-protein P12931 SRC kinase Src | SRC N1
Proto-oncogene tyrosine-protein P07947 YES1 kinase Yes
P-Selectin | CD62P P16109 SELP
Pulmonary surfactant-associated P35247 SFTPD protein D | SP-D
Pyridoxal phosphate phosphatase Q96GD0 PDXP
Pyruvate dehydrogenase kinase, Q15118 PDK1 isozyme 1
Rab GDP dissociation inhibitor β P50395 GDI2
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
RAGE, soluble | Advanced glycosylation end product-specific Q15109 AGER
receptor
RANTES | CCL5 P13501 CCL5
RAS p21 protein activator | p120GAP P20936 RASA1
Ras-related C3 botulinum toxin P63000 RAC1 substrate 1
Receptor activator of NF-KB | RANK Q9Y6Q6 TNFRSF11A
Receptor-type tyrosine-protein kinase P36888 FLT3 FLT3 | Flt-3 | Flk-2
RELT tumor necrosis factor receptor | Q969Z4 RELT TNFRSF19L
Renin P00797 REN
Repulsive guidance molecule A Q96B86 RGMA
Resistin | FIZZ3 | Adipose tissue- Q9HD89 RETN specific secretory factor | ADSF
Reticulon-4 | Nogo-A Q9NQC3 RTN4
Retinoblastoma 1 P06400 RB1
Retinol-binding protein 4 P02753 RBP4 Y
RGM domain family member B Q6NW40 RGMB
Ribosomal protein S3 P23396 RPS3
Ribosomal protein S6 kinase 5 | Mitogen- and stress-activated kinase 1 O75582 RPS6KA5
| MSK1 | RSK-like protein kinase
Ribosomal protein S6 kinase α-3 | P51812 RPS6KA3 RSK2 Ribosomal protein S7 P62081 RPS7
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
Ribosome maturation protein SBDS Q9Y3A5 SBDS
RNA-binding motif protein 39 | Q14498 RBM39 CAPER-α Roof plate-specific spondin-2, isoform Q6UXX9 RSPO2 1
Roundabout axon guidance molecule Q9HCK4 ROBO2 2, ROBO2
Roundabout axon guidance molecule Q96MS0 ROBO3 3, ROBO3
S100A9 | calgranulin B | MRP-14 P06702 S100A9 Y
Scavenger receptor class F member 1 Q14162 SCARF1 | SREC-I
Scavenger receptor class F member 2 Q96GP6 SCARF2 | SREC-II
Scavenger receptor cysteine-rich type Q86VB7 CD163 1 protein M130 chain | Soluble CD163
Scavenger receptor for phosphatidylserine and oxidized low Q9H2A7 CXCL16
density lipoprotein | CXCL16
Secretin P09683 SCT
Secretory leukocyte protease inhibitor P03973 SLPI
Seizure 6-like protein 2 Q6UXD5 SEZ6L2
Semaphorin-3A Q14563 SEMA3A
Semaphorin-3E O15041 SEMA3E
Semaphorin-6A Q9H2E6 SEMA6A
Serine/threonine kinase 17b | DRAK2 O94768 STK17B
Serine-threonine-protein kinase 16 | O75716 STK16 PKL12
Serine-threonine-protein kinase Chk1 O14757 CHEK1
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
Serine-threonine-protein kinase Chk2 O96017 CHEK2
Serine-threonine-protein kinase PLK1 P53350 PLK1
Serum amyloid A P0DJI8 SAA1
Serum amyloid P P02743 APCS
Sex hormone-binding globulin P04278 SHBG
SH2 domain-containing protein 1A | O60880 SH2D1A Y SLAM-associated protein (SAP)
SHC-transforming protein 1 P29353 SHC1
Shh receptor Boc Q9BWV1 BOC
Siglec-1 | Sialoadhesin Q9BZZ2 SIGLEC1
Siglec-14 Q08ET2 SIGLEC14
Siglec-3 P20138 CD33
Siglec-6 | CD327 O43699 SIGLEC6
Siglec-7 | CD328 Q9Y286 SIGLEC7
Siglec-9 Q9Y336 SIGLEC9
Signaling lymphocytic activation Q9UIB8 CD84 molecule 5 | SLAMF5
Sirtuin 2 Q8IXJ6 SIRT2
SLAM family member 6 | NTB-A Q96DU3 SLAMF6
SLAM family member 7 | CRACC | CS1 Q9NQ25 SLAMF7
SLIT and NTRK-like protein 5 O94991 SLITRK5
SMAC | DIABLO Q9NR28 DIABLO Y
Small glutamine-rich tetratricopeptide repeat-containing protein α | Vpu- O43765 SGTA
binding protein
Small nuclear ribonucleoprotein F P62306 SNRPF
Soggy-1 Q9UK85 DKKL1
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis Somatostatin-28 P61278 SST
Sonic hedgehog Q15465 SHH
Sortilin-related VPS10 domain Q96PQ0 SORCS2 containing receptor 2 | SorCS2
Sorting nexin 4 O95219 SNX4
SPARC-like 1 (hevin) Q14515 SPARCL1
S-phase kinase-associated protein 1 | P63208 SKP1 OCP2
Sphingomyelin phosphodiesterase, Q92484 SMPDL3A acid-like 3A | ASML3a
Sphingosine kinase 1 Q9NYA1 SPHK1
Sphingosine kinase 2 Q9NRA0 SPHK2
Spondin-1 | F-Spondin Q9HCB6 SPON1
Stabilin-2 Q8WWQ8 STAB2
Stanniocalcin-1 P52823 STC1
Stem cell factor receptor | CD117 | P10721 KIT SCF R | c-Kit
Stem cell growth factor-α Q9Y240 CLEC11A
Stem cell growth factor-β Q9Y240 CLEC11A
Stress-induced-phosphoprotein 1 P31948 STIP1
Stromal cell-derived factor 1 | SDF-1 P48061 CXCL12
SUMO-conjugating enzyme UBC9 | P63279 UBE2I UBE2I | Ubc9
Superoxide dismutase [Cu-Zn] P00441 SOD1
Superoxide dismutase [Mn] P04179 SOD2
Survivin O15392 BIRC5
Syntaxin 1A | HPC1 Q16623 STX1A
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
T cell membrane protein TIM-3 | Hepatitis A virus cellular receptor 2 | Q8TDQ0 HAVCR2
TIM-3
TACI | Transmembrane activator and O14836 TNFRSF13B CAML interactor | TNFRSF13B
TAK1-TAB1 fusion O43318, Q15750 MAP3K7 TAB1
TANK-binding kinase 1 Q9UHD2 TBK1
Tartrate-resistant acid phosphatase P13686 ACP5 type 5 | TRACP | PAP
TATA-box-binding protein P20226 TBP
T-cell surface glycoprotein CD4 P01730 CD4
Tenascin-C P24821 TNC
Testican-1 | SPOCK1 Q08629 SPOCK1
Testican-2 | SPOCK2 Q92563 SPOCK2
TFF3 | Trefoil factor 3 | Intestinal Q07654 TFF3 trefoil factor | hITF
TGF-β receptor II P37173 TGFBR2
Thioredoxin domain-containing O95881 TXNDC12 protein 12 Thrombin P00734 F2
Thrombin-activatable fibrinolysis Q96IY4 CPB2 inhibitor
Thrombopoietin receptor P40238 MPL
Thrombospondin-1 P07996 THBS1 Y Thrombospondin-2 P35442 THBS2
Thrombospondin-4 P35443 THBS4
Thymic stromal lymphopoietin Q969D9 TSLP
Thymic stromal lymphopoietin protein Q9HC73 CRLF2 receptor | TSLP R
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
Thymidine kinase 1, cytosolic P04183 TK1
Thymidylate synthase P04818 TYMS
Thymus and activation-regulated Q92583 CCL17 chemokine | TARC
Thymus expressed chemokine | TECK O15444 CCL25
Thyroglobulin P01266 TG
Thyroid peroxidase P07202 TPO
Thyroid stimulating hormone | TSH P01215, P01222 CGA TSHB
Thyroxine-binding globulin P05543 SERPINA7
TIMP1 | Tissue inhibitor of P01033 TIMP1 metalloproteinases 1
TIMP2 | Tissue inhibitor of P16035 TIMP2 metalloproteinases 2
TIMP3 | Tissue inhibitor of P35625 TIMP3 metalloproteinases 3
Tissue factor | Coagulation Factor III P13726 F3
Tissue factor pathway inhibitor P10646 TFPI
TLR4:MD-2 complex | Toll-like receptor 4:Myeloid differentiation O00206 Q9Y6Y9 TLR4 LY96
factor-2 complex
T-lymphocyte activation antigen CD80 P33681 CD80 | B7-1
T-lymphocyte surface antigen Ly-9 | Q9HBG7 LY9 CD229 | SLAMF3
TNF RI | Tumor necrosis factor P19438 TNFRSF1A receptor superfamily member 1A
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
TNF RII | Tumor necrosis factor P20333 TNFRSF1B receptor superfamily member 1B
TNF-like ligand 1A | TL1A | TNFSF15 | O95150 TNFSF15 VEGF inhibitor | VEGI
TNF-α | Tumor necrosis factor ligand P01375 TNF superfamily member 2
TNF-β | Lymphotoxin-α | Tumor necrosis factor ligand superfamily P01374 LTA
member 1
Toll-like receptor 2 O60603 TLR2
tPA | Tissue-type plasminogen P00750 PLAT activator
TRAIL R1 | Tumor necrosis factor O00220 TNFRSF10A receptor superfamily member 10A
TRAIL R4 | Tumor necrosis factor Q9UBN6 TNFRSF10D receptor superfamily member 10D
Transcription factor MLR1 | Ligand- dependent nuclear receptor Q8N3X6 LCORL
corepressor-like protein
Transferrin P02787 TF
Transforming growth factor β induced Q15582 TGFBI protein ig-h3
Transforming growth factor β receptor Q03167 TGFBR3 type III
Transforming growth factor β-1 P01137 TGFB1
Transforming growth factor β-2 P61812 TGFB2
Transforming growth factor β-3 P10600 TGFB3
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis Transglutaminase 3 Q08188 TGM3
Transketolase P29401 TKT
Triosephosphate isomerase P60174 TPI1
TROP-2 | Tumor-associated calcium P09758 TACSTD2 signal transducer 2
Tropomyosin 1 P09493 TPM1
Tropomyosin β chain P07951 TPM2
Troponin I, cardiac P19429 TNNI3
TROY | TNFRSF19 Q9NS68 TNFRSF19
Trypsin P07477 PRSS1
Trypsin-2 P07478 PRSS2
Trypsin-3 P35030 PRSS3
Tryptase β-2 P20231 TPSB2
Tryptase γ Q9NRR2 TPSG1
TSG-6 | Tumor necrosis factor- P98066 TNFAIP6 inducible gene 6 protein
TWEAK |Tumor necrosis factor ligand O43508 TNFSF12 superfamily member 12
TWEAK receptor | TNFRSF12A Q9NP84 TNFRSF12A
Tyrosine kinase 2 P29597 TYK2 Y
Tyrosine kinase Bruton Q06187 BTK
Tyrosine kinase Etk | BMX non- P51813 BMX receptor tyrosine kinase
Tyrosine kinase Fer P16591 FER
Tyrosine phosphatase SHP-1 P29350 PTPN6
Tyrosine-protein kinase 6 | Brk Q13882 PTK6
Tyrosine-protein kinase receptor Tie-1, P35590 TIE1 soluble
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
Tyrosine-protein kinase receptor Tie-2, Q02763 TEK soluble | Angiopoietin-1 receptor
Tyrosine-protein kinase receptor Q06418 TYRO3 TYRO3 | Dtk
Tyrosine-protein kinase Tec P42680 TEC
Tyrosine-protein kinase Q01973 ROR1 transmembrane receptor ROR1
Tyrosine-protein phosphatase non- P18031 PTPN1 receptor type 1 | PTP1B
Tyrosine-protein phosphatase non- Q06124 PTPN11 receptor type 11 | SHP-2
Tyrosine-protein phosphatase non- P17706 PTPN2 receptor type 2 | TC-PTP
Ubiquitin P62979 RPS27A Y
Ubiquitin C-terminal hydrolase-L1 | P09936 UCHL1 PGP9.5
Ubiquitin+1, truncated mutation for P62979 RPS27A Y UbB
Ubiquitin-conjugating enzyme E2 L3 P68036 UBE2L3
Ubiquitin-conjugating enzyme E2 N P61088 UBE2N
Ubiquitin-fold modifier 1 P61960 UFM1
Ubiquitin-fold modifier-conjugating Q9Y3C8 UFC1 enzyme 1
UL16-binding protein 1 | NKG2D Q9BZM6 ULBP1 ligand 1
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis UL16-binding protein 2 | NKG2D Q9BZM5 ULBP2 ligand 2
UL16-binding protein 3 Q9BZM4 ULBP3
UMP-CMP kinase P30085 CMPK1
uPA |Urokinase-type plasminogen P00749 PLAU activator
uPAR | Urokinase plasminogen Q03405 PLAUR activator surface receptor
v-abl Abelson murine leukemia viral P42684 ABL2 oncogene homolog 2 | ARG
Vaccinia virus VH1-related phosphatase | Dual specificity protein P51452 DUSP3
| VHR phosphatase 3
Vascular cell adhesion protein 1 | P19320 VCAM1 VCAM 1 | CD106
Vascular endothelial growth factor A | P15692 VEGFA VEGF 165
Vascular endothelial growth factor A, P15692 VEGFA secreted splice variant | VEGF 121
Vascular endothelial growth factor C P49767 VEGFC
Vascular endothelial growth factor P35968 KDR receptor 2
Vascular endothelial growth factor P35916 FLT4 receptor 3 | Flt-4
Vasoactive intestinal peptide P01282 VIP
von Willebrand factor P04275 VWF
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
WAP, kazal, immunoglobulin, kunitz and NTR domain-containing protein 2 Q8TEU8 WFIKKN2 | GDF serum-associated protein-1 | GASP-1
Wingless-type MMTV integration site O00755 WNT7A family, member 7A | Wnt-7a
Wnt inhibitory factor 1 Q9Y5W5 WIF1
WNT1-inducible-signaling pathway O95388 WISP1 Y protein 1 | WISP-1 | CCN4
X-linked ectodysplasin-A2 receptor | Q9HAV5 EDA2R SF27 | XEDAR
X-Pro aminopeptidase 1 Q9NQW7 XPNPEP1
ZAP70 | 70 kDa zeta-associated P43403 ZAP70 protein kinase
α1-Antichymotrypsin P01011 SERPINA3
α1-antichymotrypsin complex | ACT P01011 SERPINA3 complex
α1-Antitrypsin P01009 SERPINA1
α2-Antiplasmin P08697 SERPINF2
α2-HS-Glycoprotein | Fetuin A P02765 AHSG
α2-Macroglobulin P01023 A2M Y
α2-Macroglobulin receptor-associated P30533 LRPAP1 protein
αII-Spectrin | α-fodrin Q13813 SPTAN1
α-L-iduronidase P35475 IDUA
α-S1-casein P47710 CSN1S1
β2-Microglobulin P61769 B2M
© 2016 American Medical Association. All rights reserved.
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Excluded from Protein Analyte UniProt ID Gene Analysis
β-Adrenergic receptor kinase 1 | GRK2 P25098 ADRBK1
β-Endorphin P01189 POMC Y β-Nerve growth factor P01138 NGF
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3 Variable Selection and Statistical Modeling The LASSO1 was used as a variable screening procedure to identify a subset of proteins jointly associated with increased cardiovascular risk. Cross-validation using coxnet2 in the R package glmnet3 was used to set the LASSO regularization parameter. The “one standard error” rule4 was used for setting the regularization level. To establish the sensitivity of the variable selection procedure to the cross- validation process the combination of LASSO + backward elimination was repeated 100 times with different cross-validation folds and a slight variant of the data pre-processing and outlier filtering steps. With this level of perturbation 7 of the 9 proteins were included in the final model at least 95% of the time. Two proteins appear in the final model less frequently under these perturbations – one approximately 60% of the time and another only 30% of time. For context, the other LASSO-selected proteins appear in the final model fewer than 2% of the time so the proteins that comprise the 9 protein model are generally what one would find using LASSO with regularization level set using the 1-standard error rule. To generate reproducible results for the ensuing analysis the random number seed was fixed at 1 prior to LASSO cross-validation. Initializing this value and setting the LASSO regularization parameter to the value 1 standard error above that which minimized the cross-validated partial likelihood deviance resulted in a LASSO model containing the 16 proteins discussed in the main manuscript. Ideally when using LASSO for variable selection the goal should be to identify a subset of variables that is relatively insensitive to the precise LASSO regularization level. In practice some of the variables selected are more sensitive to the specific regularization level than others so the concept of “stability5,6” was used to regularization level to guide the variable subset selection. Specifically, the sensitivity of individual variables to the LASSO regularization level was quantified by calculating the empirical selection probability for each of the 1054 proteins using an adaptation of stability selection6 for Cox proportional hazards models fitted using the R function glmnet. The method involves partitioning the data and sweeping the LASSO regularization parameter across its full range in uniform (logarithmic) steps. At each step the proteins that are included in the model at that specific regularization level were tabulated. Over many such random partitions this process generated a curve giving the empirical selection probability for each protein as a function of LASSO regularization level.
Using this method the median selection probability for the 9 proteins was 0.91 indicating that half were selected at least 91% of the time in models constructed using a wide range of LASSO regularization levels. Only three of the 9 proteins had selection probabilities below 0.75 and the least stable protein was still selected more than 60% of the time.
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That most of the proteins have selection probabilities at least 0.75 provided confidence that the proteins in the 9-protein model are not particularly sensitive to the specific choice of LASSO regularization parameter.
Though the variable selection procedure was stable as discussed above, it was nonetheless still possible to create alternative protein models from the set of LASSO-selected (or stability selection) proteins. Using a more stringent data standardization procedure an alternate 9 protein model was derived that differed in a single protein from the one discussed in the text. This alternate model had similar discrimination performance but owing to the improved data standardization it did not require recalibration before application to the validation cohort.
4 Recalibration for Validation The need for prognostic model recalibration is dictated by underlying differences in the baseline survivor function in the derivation and validation cohorts. For both the refit Framingham model and 9- protein model, the “validation by calibration” program outlined in van Houwelingen7 was followed, considering both Cox and Weibull AFT recalibration models for formal recalibration assessment in the validation cohort. Based on an empirical assessment of calibration performance, the 9-protein model was recalibrated with the Weibull accelerated failure time (AFT) recalibration model of the form,
log(퐻(푡|푃퐼)) = 훾0 + 훾1푃퐼 + 훾2푒 , where PI is the prognostic index, H(t|PI) is the cumulative hazard function with error term 푒 having an
PI extreme value distribution. Denoting the baseline cumulative hazard by H0(t) and using H(t|PI) = H0(t)e gives,
log(퐻0(푡)) = 훾0 + (훾1 − 1)푃퐼 + 훾2푒 . (1)
A formal calibration assessment tests the perfect calibration hypothesis, 퐻0: 훾0 = 0, 훾1 = 0, 훾2 = 1 . Fitting the model (1) using survreg from the R package survival8 gives the calibration coefficients listed in eTable 2.
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9 Protein Model Recalibration Model Coefficients Estimate 95% CI p-value 훾̂0 -0.230 -0.4189 -0.0412 0.02
훾̂1 − 1 -0.998 -1.1752 -0.8212 0.98 log (훾̂2) 0.149 0.0384 0.2598 0.008
eTable 2: Weibull recalibration model coefficients for 9-protein model.
The estimated value for the intercept term (훾̂0) is significant (p=0.02) and the resulting “recalibrated” prognostic index and extreme value scale parameter (shown below) was used in the validation cohort
PI=16.39 -1.54×ANGPT2 + 1.22×GDF11/8 - 2.11×C7 +2.64×SERPINF2 - 0.57×CCL18 - 1.02×ANGPTL4 - 1.43×KLK3.SERPINA3 - 0.72×MMP12 - 0.59×TNNI3 { s=0.98
It is not uncommon for differences in sample collection protocol to generate a systematic intensity differences for the signal levels for a large number of proteins. Blood samples in the validation cohort were collected using a more lenient collection protocol than those in the derivation cohort resulting in a systematic difference in “bulk” signal intensity between the cohorts. The data standardization procedures in use the time these samples were assayed removed this bulk difference between the cohorts. Post-hoc it was discovered that this “pre-processing” introduced an artifact in the signal levels for the 9-model proteins. eFigure 1 shows the median signal levels for the 9 proteins in the derivation and validation cohorts before (left) and after (right) pre-processing. While the pre-processing removes the bulk intensity differences in the vast majority of proteins measured in the validation cohort, it introduces a bias in these 9 proteins which are relatively insensitive to sample collection protocol differences.
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eFigure 1: Median protein level in relative fluorescent intensity units(RFU) in Derivation and Validation cohort for before (left) and after (right) data pre-processing with multiplicative scaling to remove bulk signal intensity differences in “most” proteins between the derivation and validation cohorts.
The intercept of the robust regression line in the right frame of eFigure 1 gives an estimate of the intensity bias introduced into protein signals. If we let ̂ denote this estimate then since the 9 protein model uses standardized covariates applying the model to an observation in the validation cohort resulted in the addition of the constant factor, 9 훽푗 ∆ ∑푗=1 (2), 휎푗
to what would otherwise be the contribution of the model intercept, 훽0. As a result, the signal intensity artifact introduced by the data pre-processing appears as a discrepancy in the time scale of the baseline
survivor function in the validation cohort, precisely the term associated with the parameter 훾0 in calibration model (1). Plugging the estimate ̂ = 0.058 from eFigure 1 into (2) and using the model
coefficients and population standard deviations introduced a constant factor that differed from (훾̂0) by 0.6% indicating that in fact the data processing artifact was largely responsible for the calibration result.
It was subsequently verified that applying more stringent data pre-processing procedures prior to the statistical analysis avoids the artifact discussed above resulting in a “null” recalibration model. The resulting prognostic model can be applied directly to the validation cohort without recalibration..
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To recalibrate the Framingham variable model for use in the validation cohort a single variable Cox proportional hazard recalibration7,9 model was used. This model gave superior calibration performance compared to the AFT-calibration model used for recalibrating the 9-protein model. Denoting the
baseline survivor function by S0(t), the calibrated 4-year risk score was
̂∗ 푒훽 × 푃퐼퐹푅 Prcal[푇 ≤ 푡] = 1 − 푆̂0(4) , ∗ where 훽̂ is the estimate from the calibration model and 푆̂0(t) is the Weibull model estimate of the survivor function. The table below (eTable 3) lists the resulting calibration model coefficient:
Refit Framingham model Recalibration model coefficients Estimated Cox Calibration 푆̂(4) Standard Error p-value 0 Coefficient (훽̂∗) Recalibration Coefficient 0.752 -0.5322 0.0702 <0.0001
eTable 3: Recalibration model coefficients for refit Framingham model.
Calibration plots for recalibrated proteomic model are shown in the main text and the recalibrated refit Framingham model below (eFigure 2):
eFigure 2: Calibration plots for derivation (left) and validation (right) cohorts for the refit Framingham model. Shown is the observed vs. predicted 4-year incidence of the primary outcome by deciles of predicted risk. Predicted 4-year incidence for each decile is the mean predicted risk score in each decile. Error bars indicate standard deviation. As explained above, the refit Framingham model was recalibrated for use in the validation cohort.
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5 Table of Individual Proteins Associated with Cardiovascular Risk In this study 1054 of the 1130 proteins measured by were deemed fit for analysis and 200 were significantly associated with cardiovascular risk. These 200 proteins are listed in eTable 4 Along with each protein we list the Universal Protein Resource (UniProt) (http://www.uniprot.org) identifier and the hazard ratio (both quintile and per standard deviation) along with the p-value for the latter.
eTable 4 (below): Proteins associated with risk of MI, stroke, heart failure and death at a 5% Bonferonni corrected level (correcting for 1054 comparisons) using single protein Cox Proportional hazard model. Quintile hazard ratio is the ratio of hazard for patients in the 5th (highest) quintile risk category compared to those in the 1st (lowest) quintile risk category.
Hazard Quintile Target Full Name UniProt Ratio Hazard P value per SD Ratio
Angiopoietin-2 Angiopoietin-2 O15123 1.67 3.41 < 1.00E-16 MMP-12 Matrix metalloproteinase 12 P39900 1.65 3.71 < 1.00E-16 TIMD3 Hepatitis A virus cellular receptor 2 Q8TDQ0 1.61 3.44 < 1.00E-16 Insulin-like growth factor-binding IGFBP-2 P18065 1.58 3.35 < 1.00E-16 protein 2 Tumor necrosis factor receptor TNF sR-II P20333 1.56 3.72 < 1.00E-16 superfamily member 1B FSTL3 Follistatin-related protein 3 O95633 1.56 4.47 < 1.00E-16 HCC-1 C-C motif chemokine 14 Q16627 1.55 2.89 < 1.00E-16 b2-Microglobulin Beta-2-microglobulin P61769 1.54 4.39 < 1.00E-16 TSP2 Thrombospondin-2 P35442 1.54 3.80 < 1.00E-16 MMP-7 Matrix metalloproteinase 7 P09237 1.53 4.09 < 1.00E-16 Endostatin Endostatin P39060 1.52 2.92 < 1.00E-16 Cathepsin H Cathepsin H P09668 1.52 4.02 < 1.00E-16 EPHB2 Ephrin type-B receptor 2 P29323 1.50 2.53 < 1.00E-16 IL-18 BPa Interleukin-18-binding protein O95998 1.49 2.89 < 1.00E-16 CRDL1 Chordin-like protein 1 Q9BU40 1.49 2.80 < 1.00E-16 Cystatin C Cystatin-C P01034 1.49 3.65 < 1.00E-16 C9 Complement component C9 P02748 1.48 3.05 8.85E-14 PARC C-C motif chemokine 18 P55774 1.47 2.50 1.11E-16 C7 Complement component C7 P10643 1.47 3.84 < 1.00E-16 Tumor necrosis factor receptor RELT Q969Z4 1.47 3.72 < 1.00E-16 superfamily member 19L JAG1 Protein jagged-1 P78504 1.45 2.25 3.66E-15 UNC5H3 Netrin receptor UNC5C O95185 1.44 3.35 < 1.00E-16 Ephrin-A4 Ephrin-A4 P52798 1.44 3.70 < 1.00E-16
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Hazard Quintile Target Full Name UniProt Ratio Hazard P value per SD Ratio
BSSP4 Brain-specific serine protease 4 Q9GZN4 1.44 2.92 < 1.00E-16 Neuroblastoma suppressor of DAN P41271 1.43 3.45 < 1.00E-16 tumorigenicity 1
Epithelial cell kinase Ephrin type-A receptor 2 P29317 1.43 3.28 < 1.00E-16
Spondin-1 Spondin-1 Q9HCB6 1.42 3.20 < 1.00E-16 Periostin Periostin Q15063 1.40 2.15 6.12E-12 VEGF Vascular endothelial growth factor A P15692 1.40 2.35 1.03E-12 SREC-I Scavenger receptor class F member 1 Q14162 1.39 3.45 < 1.00E-16 alpha-1- antichymotrypsin alpha-1-antichymotrypsin complex P01011 1.39 2.50 1.97E-14 complex CRK Adapter molecule crk P46108 1.39 3.06 < 1.00E-16 Ephrin-A5 Ephrin-A5 P52803 1.37 2.62 2.89E-15 Endothelial cell-selective adhesion ESAM Q96AP7 1.37 2.27 1.02E-14 molecule Glutathione S- Glutathione S-transferase P P09211 1.37 2.57 1.28E-12 transferase Pi Tumor necrosis factor receptor DR6 O75509 1.36 1.82 1.36E-10 superfamily member 21 CAPG Macrophage-capping protein P40121 1.36 3.24 < 1.00E-16 Coiled-coil domain-containing protein URB Q76M96 1.36 2.34 1.36E-10 80 LAG-3 Lymphocyte activation gene 3 protein P18627 1.35 2.11 2.48E-10 Ck-b-8-1 Ck-beta-8-1 P55773 1.35 2.14 1.26E-08 Elafin Elafin P19957 1.35 2.45 9.14E-12 TIMP-1 Metalloproteinase inhibitor 1 P01033 1.34 3.95 < 1.00E-16 HSP 70 Heat shock 70 kDa protein 1A/1B P08107 1.34 2.21 1.25E-10 Stanniocalcin-1 Stanniocalcin-1 P52823 1.34 2.61 2.65E-11 SLPI Antileukoproteinase P03973 1.34 2.36 7.96E-11 Low affinity immunoglobulin gamma Fc FCG3B O75015 1.34 2.13 2.53E-10 region receptor III-B Tumor necrosis factor receptor TRAIL R4 Q9UBN6 1.34 2.07 1.29E-09 superfamily member 10D MMP-3 Stromelysin-1 P08254 1.33 2.49 1.37E-09 PH Pancreatic hormone P01298 1.33 2.25 1.19E-10 ARMEL Cerebral dopamine neurotrophic factor Q49AH0 1.32 1.98 5.50E-10 CYTD Cystatin-D P28325 1.32 1.99 9.40E-10 GPVI Platelet glycoprotein VI Q9HCN6 1.32 1.85 3.10E-09 CATZ Cathepsin Z Q9UBR2 1.32 2.34 9.36E-10 DLL1 Delta-like protein 1 O00548 1.32 3.40 < 1.00E-16 MPIF-1 C-C motif chemokine 23 P55773 1.31 1.99 2.74E-09
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Hazard Quintile Target Full Name UniProt Ratio Hazard P value per SD Ratio
Kallikrein 11 Kallikrein-11 Q9UBX7 1.31 2.03 1.22E-11 SLAF5 SLAM family member 5 Q9UIB8 1.31 2.60 9.99E-16 IL-1 R4 Interleukin-1 receptor-like 1 Q01638 1.31 2.08 1.92E-09 TFF3 Trefoil factor 3 Q07654 1.30 3.58 3.51E-13 Platelet-activating factor PAFAH beta subunit P68402 1.29 2.49 8.03E-14 acetylhydrolase IB subunit beta Insulin-like growth factor-binding IGFBP-1 P08833 1.29 1.90 1.12E-08 protein 1 CD48 CD48 antigen P09326 1.29 2.30 4.62E-10 Renin Renin P00797 1.29 1.77 1.68E-08 NLGNX Neuroligin-4, X-linked Q8N0W4 1.29 2.60 1.92E-12 BLC C-X-C motif chemokine 13 O43927 1.29 2.67 1.24E-11 Urokinase plasminogen activator suPAR Q03405 1.29 3.18 3.80E-13 surface receptor PAPP-A Pappalysin-1 Q13219 1.29 1.95 6.82E-08 resistin Resistin Q9HD89 1.28 1.87 2.27E-08 SDF-1 Stromal cell-derived factor 1 P48061 1.28 2.02 2.17E-07 FUT5 Alpha-(1,3)-fucosyltransferase 5 Q11128 1.28 2.04 8.33E-07 Tumor necrosis factor ligand TNFSF15 O95150 1.28 3.05 6.62E-13 superfamily member 15 Nidogen Nidogen-1 P14543 1.28 1.83 1.11E-07 HTRA2 Serine protease HTRA2, mitochondrial O43464 1.28 2.14 6.37E-09 Insulin-like growth factor-binding IGFBP-7 Q16270 1.28 1.82 1.55E-07 protein 7 IL-1 sRI Interleukin-1 receptor type 1 P14778 1.28 1.73 1.12E-06 Phospholipase A2, membrane NPS-PLA2 P14555 1.27 2.18 5.24E-09 associated ANGL4 Angiopoietin-related protein 4 Q9BY76 1.27 3.08 4.95E-11 FABP Fatty acid-binding protein, heart P05413 1.27 2.64 1.30E-10 LBP Lipopolysaccharide-binding protein P18428 1.27 2.04 1.81E-06 IGF-I sR Insulin-like growth factor 1 receptor P08069 1.27 1.84 9.91E-07 Tenascin Tenascin P24821 1.27 1.84 3.15E-07 Tumor necrosis factor receptor XEDAR Q9HAV5 1.27 3.99 < 1.00E-16 superfamily member 27 Troponin I Troponin I, cardiac muscle P19429 1.27 3.18 1.02E-12 BSP Bone sialoprotein 2 P21815 1.27 1.80 7.52E-08 Insulin-like growth factor-binding IGFBP-6 P24592 1.26 2.42 3.06E-11 protein 6 MATN2 Matrilin-2 O00339 1.26 2.12 4.44E-07 LY9 T-lymphocyte surface antigen Ly-9 Q9HBG7 1.26 1.75 1.79E-06 Layilin Layilin Q6UX15 1.26 2.84 1.43E-09
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Hazard Quintile Target Full Name UniProt Ratio Hazard P value per SD Ratio
XTP3A dCTP pyrophosphatase 1 Q9H773 1.26 1.69 7.38E-06 Fibrinogen g-chain Fibrinogen gamma chain P02679 1.25 1.88 3.30E-06 dimer EphB6 Ephrin type-B receptor 6 O15197 1.25 1.85 3.27E-09 Oxidized low-density lipoprotein OLR1 P78380 1.25 1.85 2.38E-07 receptor 1 Carbonic anhydrase Carbonic anhydrase 3 P07451 1.25 1.93 5.34E-07 III CYTT Cystatin-SA P09228 1.25 1.80 2.83E-06 FGF7 Fibroblast growth factor 7 P21781 1.25 2.78 2.90E-12 AK1A1 Alcohol dehydrogenase [NADP(+)] P14550 1.25 1.91 1.86E-06 Tyrosine-protein kinase transmembrane ROR1 Q01973 1.24 1.95 1.40E-08 receptor ROR1 Midkine Midkine P21741 1.24 2.20 2.96E-09 Low affinity immunoglobulin gamma Fc P12318 FCG2A/B 1.24 1.83 7.23E-06 region receptor II-a/b P31994 IP-10 C-X-C motif chemokine 10 P02778 1.24 2.26 1.08E-06 MBL Mannose-binding protein C P11226 1.24 1.89 1.44E-05 NAGK N-acetyl-D-glucosamine kinase Q9UJ70 1.23 1.54 4.84E-06 MCP-3 C-C motif chemokine 7 P80098 1.23 1.98 3.56E-07 SHC1 SHC-transforming protein 1 P29353 1.23 1.96 6.47E-08 GPNMB Transmembrane glycoprotein NMB Q14956 1.23 1.64 2.29E-06 Macrophage Macrophage mannose receptor 1 P22897 1.23 1.83 1.30E-05 mannose receptor Dual specificity mitogen-activated MP2K2 P36507 1.23 1.81 1.01E-05 protein kinase kinase 2 Tumor necrosis factor receptor TNF sR-I P19438 1.23 3.71 < 1.00E-16 superfamily member 1A Cathepsin B Cathepsin B P07858 1.23 1.76 5.70E-06 vWF von Willebrand factor P04275 1.23 1.74 1.49E-05 TF Tissue Factor P13726 1.23 2.78 8.34E-13 Tumor necrosis factor ligand CD30 Ligand P32971 1.22 1.46 6.40E-07 superfamily member 8 IL-17 RC Interleukin-17 receptor C Q8NAC3 1.22 2.56 3.50E-09
Nectin-like protein 2 Cell adhesion molecule 1 Q9BY67 1.22 1.80 1.10E-05
CCL28 C-C motif chemokine 28 Q9NRJ3 1.22 1.64 1.94E-05 IL-18 Ra Interleukin-18 receptor 1 Q13478 1.22 1.58 2.90E-05 NRP1 Neuropilin-1 O14786 1.22 1.94 4.17E-08 LAG-1 C-C motif chemokine 4-like Q8NHW4 1.22 1.51 4.69E-06 Retinoic acid receptor responder TIG2 Q99969 1.22 1.80 1.58E-05 protein 2 sICAM-5 Intercellular adhesion molecule 5 Q9UMF0 1.21 1.91 1.79E-06
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Hazard Quintile Target Full Name UniProt Ratio Hazard P value per SD Ratio
CD5L CD5 antigen-like O43866 1.21 1.62 1.06E-05 BNP-32 Brain natriuretic peptide 32 P16860 1.21 2.77 1.34E-09 EGF-like module-containing mucin-like EMR2 Q9UHX3 1.21 1.82 3.46E-05 hormone receptor-like 2 Neurogenic locus notch homolog Notch-3 Q9UM47 1.21 1.88 9.13E-07 protein 3 C34 gp41 HIV gp41 C34 peptide, HIV Q70626 1.21 1.72 2.56E-06 Fragment CYTN Cystatin-SN P01037 1.20 1.52 3.97E-05 B7-H1 Programmed cell death 1 ligand 1 Q9NZQ7 1.20 2.12 3.37E-06 YES Tyrosine-protein kinase Yes P07947 1.20 2.11 9.06E-08 IL-15 Ra Interleukin-15 receptor subunit alpha Q13261 1.19 3.21 4.51E-10 P31946, P62258, P61981, 14-3-3 14-3-3 protein family Q04917, 1.19 1.75 4.45E-05 P27348, P63104, P31947 OX2G OX-2 membrane glycoprotein P41217 1.19 1.44 2.85E-05 IL-8 Interleukin-8 P10145 1.19 2.10 1.60E-07 JAM-B Junctional adhesion molecule B P57087 1.19 1.73 1.95E-06 LIF sR Leukemia inhibitory factor receptor P42702 1.19 1.72 4.55E-05 FGF23 Fibroblast growth factor 23 Q9GZV9 1.18 2.41 7.74E-08 Tumor necrosis factor receptor 4-1BB Q07011 1.18 2.36 2.83E-08 superfamily member 9 MIP-1a C-C motif chemokine 3 P10147 1.18 2.42 1.53E-06 Factor D Complement factor D P00746 1.18 2.72 3.93E-07 Tumor necrosis factor receptor TAJ Q9NS68 1.18 2.16 1.99E-07 superfamily member 19 LD78-beta C-C motif chemokine 3-like 1 P16619 1.18 1.55 3.25E-05 SPINT2 Kunitz-type protease inhibitor 2 O43291 1.17 2.18 4.28E-06 PTHrP Parathyroid hormone-related protein P12272 1.17 1.51 3.45E-05 Ubiquitin-fold modifier-conjugating UFC1 Q9Y3C8 1.17 1.41 4.54E-05 enzyme 1 VEGF-C Vascular endothelial growth factor C P49767 1.16 2.49 7.62E-06 SLAF6 SLAM family member 6 Q96DU3 1.15 1.88 3.84E-05 MIS Muellerian-inhibiting factor P03971 0.84 0.50 6.70E-06 Antithrombin III Antithrombin-III P01008 0.84 0.55 2.07E-05 FCN2 Ficolin-2 Q15485 0.83 0.59 8.21E-06 Dual specificity mitogen-activated MP2K4 P45985 0.82 0.53 1.11E-05 protein kinase kinase 4 ASAH2 Neutral ceramidase Q9NR71 0.82 0.54 4.48E-05
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Hazard Quintile Target Full Name UniProt Ratio Hazard P value per SD Ratio
Endothelin- converting enzyme Endothelin-converting enzyme 1 P42892 0.82 0.60 4.05E-05 1 Neurogenic locus notch homolog Notch 1 P46531 0.82 0.60 1.71E-05 protein 1 Heparin cofactor II Heparin cofactor 2 P05546 0.82 0.57 9.33E-06 Carbonic anhydrase Carbonic anhydrase 6 P23280 0.82 0.58 1.13E-05 6 Testican-1 Testican-1 Q08629 0.81 0.59 2.80E-05 PAI-1 Plasminogen activator inhibitor 1 P05121 0.81 0.60 1.27E-05
6-Phosphogluconate 6-phosphogluconate dehydrogenase, P52209 0.81 0.59 8.60E-06 dehydrogenase decarboxylating
Afamin Afamin P43652 0.81 0.44 7.50E-09 DRAK2 Serine/threonine-protein kinase 17B O94768 0.80 0.57 2.65E-05 Ectonucleoside triphosphate ENTP5 O75356 0.80 0.57 2.51E-06 diphosphohydrolase 5 Coagulation Factor Coagulation factor Xa P00742 0.80 0.48 3.43E-08 Xa Plasminogen Plasminogen P00747 0.80 0.58 7.86E-06 MDHC Malate dehydrogenase, cytoplasmic P40925 0.80 0.50 2.23E-06 Prothrombin Prothrombin P00734 0.80 0.44 4.72E-08 Opioid-binding protein/cell adhesion OBCAM Q14982 0.80 0.56 1.13E-05 molecule Aminoacylase-1 Aminoacylase-1 Q03154 0.80 0.52 8.51E-06 cGMP-stimulated cGMP-dependent 3',5'-cyclic O00408 0.79 0.57 3.51E-06 PDE phosphodiesterase Cytochrome P450 Cytochrome P450 3A4 P08684 0.79 0.48 1.97E-06 3A4 Ficolin-3 Ficolin-3 O75636 0.78 0.51 2.13E-08 Superoxide dismutase [Mn], Mn SOD P04179 0.78 0.52 7.13E-07 mitochondrial a2-HS-Glycoprotein Alpha-2-HS-glycoprotein P02765 0.78 0.48 1.16E-07 TrkB BDNF/NT-3 growth factors receptor Q16620 0.78 0.59 2.78E-06 C-type lectin domain family 4 member DC-SIGNR Q9H2X3 0.77 0.53 2.20E-08 M A disintegrin and metalloproteinase ATS13 Q76LX8 0.77 0.42 4.14E-09 with thrombospondin motifs 13 Kallistatin Kallistatin P29622 0.77 0.51 1.15E-08 Tyrosine-protein phosphatase non- PTP-1B P18031 0.77 0.52 6.46E-06 receptor type 1 FGF-20 Fibroblast growth factor 20 Q9NP95 0.76 0.50 1.13E-06 Cathepsin V Cathepsin L2 O60911 0.76 0.48 1.80E-08 Prekallikrein Plasma kallikrein P03952 0.76 0.49 1.99E-10
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Hazard Quintile Target Full Name UniProt Ratio Hazard P value per SD Ratio
NXPH1 Neurexophilin-1 P58417 0.75 0.57 1.11E-08 Soggy-1 Dickkopf-like protein 1 Q9UK85 0.75 0.48 2.58E-08 15-hydroxyprostaglandin HPG- P15428 0.75 0.44 1.93E-08 dehydrogenase [NAD(+)] Protein C Vitamin K-dependent protein C P04070 0.74 0.36 1.30E-13 SEPR Seprase Q12884 0.74 0.46 1.47E-06 Tumor necrosis factor ligand TWEAK O43508 0.74 0.44 4.07E-06 superfamily member 12 Vascular endothelial growth factor VEGF sR2 P35968 0.74 0.41 2.22E-10 receptor 2 Angiostatin Angiostatin P00747 0.73 0.41 5.92E-11
ERBB3 Receptor tyrosine-protein kinase erbB-3 P21860 0.72 0.38 2.04E-10
GDF-11/8 Growth/differentiation factor 11/8 O95390 0.72 0.41 8.79E-09 BMP-1 Bone morphogenetic protein 1 P13497 0.71 0.37 2.54E-13 Cell adhesion molecule-related/down- CDO Q4KMG0 0.70 0.37 9.14E-14 regulated by oncogenes CK-MM Creatine kinase M-type P06732 0.70 0.43 3.61E-11 CNDP1 Beta-Ala-His dipeptidase Q96KN2 0.69 0.33 < 1.00E-16 Dual 3',5'-cyclic-AMP and -GMP PDE11 Q9HCR9 0.69 0.36 5.19E-12 phosphodiesterase 11A Creatine kinase M-type:Creatine kinase P12277 CK-MB 0.69 0.36 5.08E-13 B-type heterodimer P06732 P-Cadherin Cadherin-3 P22223 0.67 0.39 1.11E-16 Proto-oncogene tyrosine-protein kinase RET P07949 0.66 0.38 4.93E-13 receptor Ret a2-Antiplasmin Alpha-2-antiplasmin P08697 0.64 0.34 < 1.00E-16 Growth hormone Growth hormone receptor P10912 0.63 0.27 < 1.00E-16 receptor ERBB1 Epidermal growth factor receptor P00533 0.60 0.27 < 1.00E-16
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5.1 Biological Functions of 16 LASSO-Selected Proteins The protein biomarkers identified in this analysis not only serve to derive a cardiovascular risk prediction model, but also inform understanding of the biology of cardiovascular disease (CVD) and identify potential drug targets and treatment options. Below, a brief description is provided of the known function(s) of the 16 proteins selected by LASSO.
GROWTH AND REMODELING Growth Differentiation Factor 11/8 (GDF11/8) is an example of biological discovery using unbiased proteomics assay tool with findings of potential clinical significance. Using modified aptamers, Lee and colleagues pinpointed age-related decline in circulating GDF-11 as the cause of age-related cardiac hypertrophy in mice10. GDF-11 is currently under active investigation for its role in suppressing cardiac hypertrophy and diastolic heart failure in humans. Interestingly, while GFD-11 concentrations are reduced with increasing cardiovascular event risk in this study, an inhibitor of GDF11, Follistatin-like 3 is positively associated with increasing cardiovascular risk (eTable 4). As the modified aptamer used in the present study does not distinguish GDF11 from its close homologue GDF8 as two the proteins are 90% identical in their active mature regions and have identical functions in vitro, this protein is designated as GDF11/811. Epidermal Growth Factor (EGF) receptor (EGFR) is expressed on monocytes and macrophages in atherosclerotic lesions. Activation by ligand binding stimulates cellular proliferation and chemotaxis12. Evidence from animal studies shows that EGF receptor protects against cardiac hypertrophy and supports appropriate vascular wall architecture and vessel reactivity13. Soluble forms of the Growth hormone receptor (GHR) and the epidermal growth factors can serve as both reservoirs and inhibitors of the circulating factors involved in mitogenesis, cell function, and have well-known roles in cancer. Interestingly, growth hormone receptor signaling, via stimulation of its anabolic mediator Insulin-like growth factor I, has previously been shown to have a negative correlation with risk of developing coronary artery disease14. Angiopoietin-2 (ANGPT2), which antagonizes Angiopoietin-1 activity on the Tyrosine-protein kinase receptor Tie-2 receptor and acts in concert with Angiopoietin-1 during angiogenesis, promotes relaxation of cell-matrix contacts and may induce endothelial cell apoptosis and vessel disruption during angiogenesis15. A member of the same gene family, Angiopoietin-related Protein 4 (ANGPTL4) is induced by hypoxia and not only affects vascular function and matrix-endothelial cell interaction, but also lipid metabolism as a potent inhibitor of lipoprotein lipase16.
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Controlled interactions of the extracellular matrix and cells are vital for normal organ physiology, during normal development, in response to vascular and myocardial injury, and during cancer metastasis. Matrix metalloproteinases and their inhibitors have several targets in the vascular extracellular matrix and have been associated with atherosclerotic plaque stability, aneurysm formation and other cardiovascular diseases17. Matrix metalloproteinase (MMP)-7 and MMP-12 are represented in the LASSO selected 16 proteins, while the metalloproteinase inhibitor TIMP1 also has significant association with cardiovascular risk (eTable 4). Thrombospondin-2 (THBS2) mediates vascular and cardiac cell-cell and cell-matrix interactions and has been implicated in the regulation of angiogenesis, thrombosis, and inflammation. Increased serum Thrombospondin-2 concentration is associated with the risk of cardiac mortality in older men18. Cell adhesion oncogene-related CDO (CDON) is a cell surface protein member of the Ig/fibronectin superfamily involved in myogenesis and muscle cell adhesion19. Its role in cell-cell interaction has been noted in tumor invasiveness but little is known about its relationship to the cardiovascular system.
INFLAMMATION Representing the complex roles of inflammation and immunity in cardiovascular disease, the 9-protein model incorporates the inflammatory chemokine Chemokine (C-C motif) ligand 18, previously known as Pulmonary and activation-regulated chemokine CCL18/PARC , which is a monocyte/macrophage- elaborated chemokine that appears to be involved in the recruitment of T cells20. Plasma levels of CCL18/PARC are elevated during episodes of unstable angina and have also been found to predict CV events in patients with stable angina21. The T-cell immunoglobulin and mucin domain-containing protein 3 (TIM-3) is involved in macrophage activation and other immune system activities22. Complement C7 (C7) is one of the 5 components that form the bioactive terminal complement complex (TCC). TCC deposited on endothelial cells results in cell proliferation, release of growth factors and inflammatory cytokines, and increased expression of tissue factor. TCC also stimulates proliferation of smooth muscle cells in atherosclerotic plaques23. In patients with symptomatic heart failure elevated serum soluble TCC predicts adverse outcome (death, urgent heart transplantation, or hospitalization with worsening heart failure)24. Complement C9, another member of TCC, is also elevated in our study.
PROTEASES
α1-antichymotrypsin complex (SERPINA3) complex represents the bound form of the protease inhibiter α1-Antichymotrypsin which has several biological substrates. It can modulate multiple acute
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and chronic disease processes including blood pressure25. α2-Antiplasmin (SERPINF2) is a serine protease inhibitor (SERPIN) that inactivates plasmin and thus reduces fibrinolysis26,27. Cathepsin H (CTSH) is a lysosomal cysteine proteinase important in the degradation of lysosomal proteins28. However, its relationship to CV disease until the present study has been uncertain29.
MYOCARDIAL NECROSIS MARKER Unlike many of the aforementioned proteins that are potentially involved in causal pathways of cardiovascular diseases, Troponin I is a well-established marker of end-organ damage (cardiomyocyte necrosis) and of cardiovascular risk30-33.
Univariate hazard ratios for the 16 LASSO selected proteins were largely consistent across the cohorts. The univariate hazard ratios per standard deviation for each of the 16 LASSO selected proteins are shown in eFigure 3 for the derivation (black) and validation (red) cohorts. Proteins included in the 9- protein model are denoted with (*).
eFigure 3: Hazard ratios (per standard deviation) for primary end-point of MI, stroke, heart failure and death with LASSO selected proteins in derivation (black) (n=938) and validation (red) cohort (n=971). Proteins marked with asterisks are included in the final 9 protein model after step-wise backwards elimination of the least important 7 proteins. Legend: MMP-7 = matrix metalloproteinase 7; MMP-12 = matrix metalloproteinase 12; TIM3 = T-cell immunoglobulin and mucin domain-containing protein 3; CCL18 = Chemokine (C-C motif) ligand 18, previously known as PARC = Pulmonary and activation-
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regulated chemokine; GDF11/8 = Growth differentiation factors 11 and 8; CDO = Cell adhesion associated oncogene regulated; EGF Receptor = epidermal growth factor receptor.
5.2 9-Protein Model Specification LASSO was used for variable selection only, as the fully parametric (Weibull) survival model was preferred as a final prognostic model. The latter has a simple representation and a mathematical form amenable7,34 to recalibration for use in external validation studies. Stepwise backward elimination starting from the full set of 16 LASSO-selected proteins was used to remove proteins from the Weibull model that were not significant predictors in the absence of the constraint imposed by the LASSO penalty. When using the Bayesian information criterion (BIC) stopping criteria to balance model performance and complexity, backward elimination discarded 7 proteins: Cathepsin H, EGF receptor, Growth hormone receptor, T cell membrane protein TIM-3, MMP-7, Cell adhesion oncogene-related CDO and Thrombospondin-2 resulting in the final 9-protein model.
For an accelerated failure time model, the probability of an event occurring at time T in the interval [0,t] is given by
퐿표푔(푡)−푃퐼 ( ) Pr[푇 ≤ 푡] = 1 − 푒−푒 푠 , where PI is the prognostic index (or linear predictor) and s is the associated extreme value distribution scale parameter. When fitting the model standardized variables were used. Absorbing the population mean and standard deviations for the proteins into the intercept term, the prognostic index (PI) and scale factor for the model applied to the derivation cohort are,
PI = 16.61-1.55×ANGPT2 + 1.22×GDF11/8 - 2.12×C7 + 2.64×SERPINF2 - 0.57×CCL18 - 1.02×ANGPTL4 - 1.43×SERPINA3 - 0.72×MMP12 - 0.59×TNNI3, s = 0.85 , where signal levels associated with the specified proteins are in taken to be in log10 relative fluorescence units(RFU). Legend: ANGPT2=Angiopoietin-2; GDF11/8=growth differentiation factor 11/8; C7=complement 7; SERPINF2= α2-antiplasmin; CCL18= chemokine (C-C motif) ligand 18; ANGPTL4= angiopoietin-related protein 4; SERPINA3= α1-antichymotrypsin complex; MMP12= matrix metalloproteinase-12; and TNNI3= troponin I.
While adjusting this model for clinical variables improved the fit slightly, these adjustments failed to produce a meaningful improvement in either the discrimination or calibration performance over that
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achieved with the “proteins only” model in the derivation cohort. Anticipating that this model might be refined based on the outcome of the validation results presented here (and additional studies in progress), various adjusted models in the main text are not presented at this time. The adjusted hazard ratio of the 9-protein model (listed above), with Prognostic index (PI) computed in the total (derivation + validation) cohort is shown in eFigure 4. The top dashed line separates the addition of Framingham variables from proteins alone and bottom dashed line separates proteins + Framingham variables + CRP, where adjustment was made for CRP for illustrative purposes as measurement of this protein is used in clinical practice.
eFigure 4: Hazard ratios (95% CI) associated with 9-protein model Prognostic Index (PI) for the primary end-point of MI, stroke, heart failure and death computed for the total (derivation + validation) cohort, adjusted for each of the Framingham variables (between dashed lines) and finally for CRP, in addition to the Framingham variables.
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6 Risk Score Distributions by Event Type The eFigure 5 below shows the distributions of 9-protein risk scores for participants with the specific cardiovascular endpoints: heart failure (CHF), myocardial infarction (MI), stroke, and death compared to participants without events (No Event) and participants that experienced any one of the events.
eFigure 5: Distributions of 9-protein risk score for participants with specific cardiovascular events in derivation (left) and validation (right). Legend: heart failure (CHF), myocardial infarction (MI).
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7 References References
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